Protein target profile

VK055_3124

UDP-N-acetylenolpyruvoylglucosamine reductase

Genome: KpATCC43816 Gene: AIK81701.1 murB 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GPZ2

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Length 342

Pocket druggability 0.027

Metabolic reactions 1

Chokepoint Yes

Direct ligand evidence 0 39 total records

Functional annotation 1 EC 8 GO

Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Metabolic bottleneck Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Central metabolic position More central than 94.9% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Review the complete evidence below

Risks to review

Microbiome similarity 132 of 4744 screened genomes (2.8%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.03.

Evidence coverage

Core evidence streams are available for this target.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target: No hit
Gut microbiome similarity: 2.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 78.947 Higher values support similarity to known essential genes.
DEG E-value: 0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization: CytoplasmicMembrane

Structure confidence

ColabFold pLDDT: 97.62 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.027

Structure A0A0H3GPZ2

Pocket Pocket 14

P2Rank 0.977

Structure A0A0H3GPZ2

Pocket Pocket 1

ColabFold model

FPocket 0.905 · Pocket 8

P2Rank 0.979 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 132 / 4744 genomes with a hit

Prevalence 2.8%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GPZ2

Pathways

KEGG R03192 BioCyc UDPNACETYLMURAMATEDEHYDROG-RXN

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Attractive metabolic target: catalyzes a producing & consuming chokepoint reaction in Amino sugar and nucleotide sugar metabolism, no isoenzyme backup detected, more central than 94.9% of genes in this genome, no human homolog detected.

Relative network centrality 94.9% more central than 94.9% of genes in this genome

Chokepoint Chokepoint gene

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MNHSLKPWNTFGIERFAKTIVRAETEQQLLSAWQTAAAAGEPTLILGEGSNVLFLNDYAGTVILNRIMGIEVSETPEAWRLHVGAGENWHQLVQFTLQHAMPGLENLALIPGCAGSSPIQNIGAYGVELQRVCEYVDCIELETGRKQRLSAAECRFGYRDSIFKHEYQDRYAIVAIGLSLAKTWQPVLSYGDLTRLDPQTVTPQQVFDAVCHMRMTKLPDPKINGNAGSFFKNPIVSAQVAEALLAQFPHAPHYPQANGSVKLAAGWLIDQCELKGQRIGGAAVHRQQALVLINEDRATSEDVVKLAHYVRQRVGAKFDVWLQPEVRFIGTHGEVNAEESIA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1.3.1.98

Gene Ontology (GO)

GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
GO:0008762 Catalysis of the reaction: UDP-N-acetylmuramate + NADP+ = UDP-N-acetyl-3-O-(1-carboxyvinyl)-D-glucosamine + NADPH + H+.
GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
GO:0009252 The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
GO:0008360 Any process that modulates the surface configuration of a cell.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

23 records

Show feature table

Start	End	DB	Term	Name
69	218	FunFam	G3DSA:3.30.465.10:FF:000018	UDP-N-acetylenolpyruvoylglucosamine reductase
69	218	Gene3D	G3DSA:3.30.465.10	-
69	218	InterPro	IPR016169	FAD-binding, type PCMH, subdomain 2
5	330	NCBIfam	TIGR00179	UDP-N-acetylmuramate dehydrogenase
5	330	InterPro	IPR003170	UDP-N-acetylenolpyruvoylglucosamine reductase
3	197	SUPERFAMILY	SSF56176	FAD-binding/transporter-associated domain-like
3	197	InterPro	IPR036318	FAD-binding, type PCMH-like superfamily
19	148	Pfam	PF01565	FAD binding domain
19	148	InterPro	IPR006094	FAD linked oxidase, N-terminal
13	183	ProSiteProfiles	PS51387	PCMH-type FAD-binding domain profile.
13	183	InterPro	IPR016166	FAD-binding domain, PCMH-type
1	68	Gene3D	G3DSA:3.30.43.10	-
1	68	InterPro	IPR016167	FAD-binding, type PCMH, subdomain 1
219	342	Gene3D	G3DSA:3.90.78.10	-
219	342	InterPro	IPR036635	UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain superfamily
1	342	Hamap	MF_00037	UDP-N-acetylenolpyruvoylglucosamine reductase [murB].
1	342	InterPro	IPR003170	UDP-N-acetylenolpyruvoylglucosamine reductase
202	339	SUPERFAMILY	SSF56194	Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain
202	339	InterPro	IPR036635	UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain superfamily
206	329	Pfam	PF02873	UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain
206	329	InterPro	IPR011601	UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal
2	329	PANTHER	PTHR21071	UDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE REDUCTASE
2	329	InterPro	IPR003170	UDP-N-acetylenolpyruvoylglucosamine reductase

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

Download VMD script Full viewer

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Pocket score High Medium Low

How colors and pocket overlays are used

Uniform protein color marks the displayed model as a single molecular object.

Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.

Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.

'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.

'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.

'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.

Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1

0.977

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Surrounding area

Site 2 P2Rank #2

0.171

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Surrounding area

Site 3 P2Rank #3

0.05

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Surrounding area

Site 4 P2Rank #4

0.04

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Surrounding area

Residue sets

UniProt: Active site:159-159

UniProt: Active site:229-229 Proton donor

UniProt: Active site:325-325

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1

0.979

Likely same site as FPocket 8 6.0 Å 31 shared residues 74% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.168

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Surrounding area

Site 3 P2Rank #3

0.023

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Surrounding area

All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold DB AF_A0A0H3GPZ2	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_3124	ColabFold	—	—	full sequence	—	Loaded

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

39 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 4 records from similar proteins

Structural ligands 4 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 35 similarity-based ZINC candidates

Best available ligand signal

973 PDB via homolog 348.8 Da · LogP 5.36 · TPSA 46.5 Open detail RCSB PDB

B3P PDB via homolog Detail RCSB PDB

EEB PDB via homolog Detail RCSB PDB

EPU PDB via homolog Detail RCSB PDB

ZINC4521259 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
973 RCSB PDB	2Q85	P08373	348.8 Da LogP 5.36 TPSA 46.5	1 viol.	✓ Clean	`c1ccc2c(c1)cccc2\C=C/3\C(=C(C(=O)O3)c4ccc(cc4)C…`
B3P RCSB PDB	4JAY	Q9HZM7	282.3 Da LogP -4.01 TPSA 145.4	1 viol.	✓ Clean	`C(CNC(CO)(CO)CO)CNC(CO)(CO)CO`
EEB RCSB PDB	1MBB	P08373	693.4 Da LogP -3.76 TPSA 332.2	3 viol.	✓ Clean	`CCC(C(=O)O)O[C@@H]1[C@H]([C@H](O[C@@H]([C@H]1O)…`
EPU RCSB PDB	1UXY	P08373	677.4 Da LogP -4.03 TPSA 332.2	3 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1O[P@@]…`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC4521259 ZINC	1.000	282.3 Da LogP -4.01 TPSA 145.4	1 viol.	✓ Clean	`OCC(CO)(CO)NCCCNC(CO)(CO)CO`
ZINC115591405 ZINC	0.636	373.6 Da LogP 4.55 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCCCNC(CO)(CO)CO`
ZINC115591837 ZINC	0.636	317.5 Da LogP 2.99 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCNC(CO)(CO)CO`
ZINC143575268 ZINC	0.636	289.5 Da LogP 2.21 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(CO)(CO)CO`
ZINC2322313 ZINC	0.636	233.4 Da LogP 0.65 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCNC(CO)(CO)CO`
ZINC97996983 ZINC	0.636	345.6 Da LogP 3.77 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCNC(CO)(CO)CO`
ZINC1611594 ZINC	0.583	243.3 Da LogP -2.43 TPSA 127.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC(CO)(CO)CO`
ZINC5273895 ZINC	0.583	257.3 Da LogP -2.04 TPSA 127.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC(CO)(CO)CO`
ZINC12959005 ZINC	0.551	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)(O)…`
ZINC12959016 ZINC	0.551	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@](=O)(O)O[P@](=O)(O…`
ZINC13548378 ZINC	0.551	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC25726233 ZINC	0.551	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@](=O)(O)O[P@](=O)(O)…`
ZINC3861755 ZINC	0.551	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC3875255 ZINC	0.551	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC3875256 ZINC	0.551	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)…`
ZINC3875257 ZINC	0.551	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC3875258 ZINC	0.551	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)…`
ZINC88466482 ZINC	0.551	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC35636069 ZINC	0.545	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)OP(=O)(O)O)[…`
ZINC40655887 ZINC	0.545	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)OP(=O)(O)O)[…`
ZINC40655889 ZINC	0.545	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC44460318 ZINC	0.545	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC4490939 ZINC	0.545	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC8585026 ZINC	0.545	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC8585028 ZINC	0.545	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O…`
ZINC8585030 ZINC	0.545	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC8585032 ZINC	0.545	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O…`
ZINC102211562 ZINC	0.537	490.3 Da LogP -1.89 TPSA 206.8	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…`
ZINC110347779 ZINC	0.537	490.3 Da LogP -1.89 TPSA 206.8	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC110347782 ZINC	0.537	490.3 Da LogP -1.89 TPSA 206.8	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC97976147 ZINC	0.537	490.3 Da LogP -1.89 TPSA 206.8	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC218568202 ZINC	0.530	498.2 Da LogP -1.85 TPSA 253.4	2 viol.	✓ Clean	`CO[C@H]1[C@@H](n2ccc(=O)[nH]c2=O)O[C@@H](CO[P@@…`
ZINC40576927 ZINC	0.530	498.2 Da LogP -1.85 TPSA 253.4	2 viol.	✓ Clean	`CO[C@@H]1[C@H](O)[C@@H](CO[P@@](=O)(O)O[P@@](=O…`
ZINC44588 ZINC	0.522	272.3 Da LogP 4.51 TPSA 26.3	✓ Ro5	✓ Clean	`O=C1O/C(=C\c2cccc3ccccc23)c2ccccc21`
ZINC1530141 ZINC	0.500	229.3 Da LogP -2.82 TPSA 127.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC(CO)(CO)CO`

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.

VK055_3124

Strong target candidate with converging metabolic, structural and chemical evidence.

Main supporting evidence

Risks to review

Evidence coverage

Prioritization evidence

Off-target risk

Essentiality

Localization

Structure confidence

Binding-site evidence

Cross-references

Sequence

Pathways

Metabolic context

Sequence

Functional annotations

Enzyme Commission (EC)

Gene Ontology (GO)

Sequence domains and features

3D structure

Binding pockets · P2Rank

Binding pockets · FPocket

Binding pockets · P2Rank

Structural evidence

Ligand evidence