Protein target profile

VK055_2476

UDP-N-acetylmuramate--alanine ligase

Genome: KpATCC43816 Gene: AIK81073.1 murC 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GI71
Length 476
Pocket druggability 0.874
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 68 total records
Functional annotation 1 EC 9 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.

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
5.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
95.83 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 0.874
Structure A0A0H3GI71
Pocket Pocket 1
P2Rank 0.98
Structure A0A0H3GI71
Pocket Pocket 1
ColabFold model
FPocket 0.893 · Pocket 2
P2Rank 0.97 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 272 / 4744 genomes with a hit
Prevalence 5.7%

Cross-references

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

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a producing chokepoint reaction in Peptidoglycan biosynthesis, no isoenzyme backup detected, more central than 90.3% of genes in this genome, no human homolog detected.

Relative network centrality 90.3% more central than 90.3% of genes in this genome
Chokepoint Chokepoint gene
Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MRRVRHIHFVGIGGAGMGGIAEVLANEGYQISGSDLAPNPVTQQLSQLGATIYFNHRPENVRDASVVVVSSAISADNPEIVAAHEARIPVIRRAEMLAELMRFRHGIAIAGTHGKTTTTAMVSSIYAEAGLDPTFVNGGLVKAAGVHARLGHSRYLIAEADESDASFLHLQPMVAIVTNIEADHMDTYHGDFENLKQTFINFLHNLPFYGRAVMCVDDPVIRELLPRVGRQITTYGFSDDADVRVEDYRQVGAQGHFRLVRQDKAILQVTLNAPGRHNALNAAAAVAVATEEGIDDRAILRALESFQGTGRRFDFLGEFPLAEVNGKPGSAMLIDDYGHHPTEVDATIKAARAGWPDKNLVMVFQPHRYTRTRDLYDDFANVLTQVDALLMLDVYPAGEAPIPGADSRSLCRTIRGRGKVDPILVPDSAQAAEMLASVLTGNDLVLVQGAGNIGKIARHLAEIKLIPQKTEEERHG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
  • GO:0016881 Catalysis of the ligation of an acid to an amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
  • GO:0008763 Catalysis of the reaction: L-alanine + ATP + UDP-N-acetylmuramate = ADP + 2 H+ + phosphate + UDP-N-acetylmuramoyl-L-alanine.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • 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.

24 records
Show feature table
Start End DB Term Name
109 289 Pfam PF08245 Mur ligase middle domain
109 289 InterPro IPR013221 Mur ligase, central
308 461 SUPERFAMILY SSF53244 MurD-like peptide ligases, peptide-binding domain
308 461 InterPro IPR036615 Mur ligase, C-terminal domain superfamily
1 92 FunFam G3DSA:3.40.50.720:FF:000046 UDP-N-acetylmuramate--L-alanine ligase
1 92 Gene3D G3DSA:3.40.50.720 -
1 462 PANTHER PTHR43445 UDP-N-ACETYLMURAMATE--L-ALANINE LIGASE-RELATED
322 403 Pfam PF02875 Mur ligase family, glutamate ligase domain
322 403 InterPro IPR004101 Mur ligase, C-terminal
310 476 FunFam G3DSA:3.90.190.20:FF:000001 UDP-N-acetylmuramate--L-alanine ligase
4 466 Hamap MF_00046 UDP-N-acetylmuramate--L-alanine ligase [murC].
4 466 InterPro IPR005758 UDP-N-acetylmuramate--L-alanine ligase
93 309 Gene3D G3DSA:3.40.1190.10 -
93 309 InterPro IPR036565 Mur-like, catalytic domain superfamily
310 476 Gene3D G3DSA:3.90.190.20 -
310 476 InterPro IPR036615 Mur ligase, C-terminal domain superfamily
93 309 FunFam G3DSA:3.40.1190.10:FF:000001 UDP-N-acetylmuramate--L-alanine ligase
5 91 SUPERFAMILY SSF51984 MurCD N-terminal domain
90 307 SUPERFAMILY SSF53623 MurD-like peptide ligases, catalytic domain
90 307 InterPro IPR036565 Mur-like, catalytic domain superfamily
6 103 Pfam PF01225 Mur ligase family, catalytic domain
6 103 InterPro IPR000713 Mur ligase, N-terminal catalytic domain
6 460 NCBIfam TIGR01082 UDP-N-acetylmuramate--L-alanine ligase
6 460 InterPro IPR005758 UDP-N-acetylmuramate--L-alanine ligase

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.

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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 · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1
0.874
Likely same site as P2Rank 1 2.1 Å 53 shared residues 88% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.98
Likely same site as FPocket 1 2.1 Å 53 shared residues 88% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.188
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.042
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.027
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.026
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:121-127
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_A0A0H3GI71
AlphaFold DB full sequence Viewing
ColabFold VK055_2476
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.

68 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 18 records from similar proteins
Structural ligands 18 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
051 PDB via homolog 526.5 Da · LogP 3.66 · TPSA 153.8 Open detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
AZI PDB via homolog Detail RCSB PDB
D17 PDB via homolog Detail RCSB PDB
EPU PDB via homolog Detail RCSB PDB

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
051 RCSB PDB P14900 526.5 Da LogP 3.66 TPSA 153.8 1 viol. ✓ Clean c1cc(c(cc1C#N)F)COc2ccc3cc(ccc3c2)S(=O)(=O)NC4C…
ANP RCSB PDB B7GV74 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AZI RCSB PDB P14900 42.0 Da LogP 0.87 TPSA 58.7 ✓ Ro5 Alert [N-]=[N+]=[N-]
D17 RCSB PDB P14900 499.6 Da LogP 2.84 TPSA 144.8 ✓ Ro5 Alert c1cc(cc(c1)C(=O)N[C@@H](CCC(=O)O)C(=O)O)CNc2ccc…
EPU RCSB PDB P45066 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@@]…
IK4 RCSB PDB P14900 468.5 Da LogP 2.89 TPSA 153.8 ✓ Ro5 ✓ Clean c1cc(ccc1COc2ccc3ccc(cc3c2)S(=O)(=O)NC(CCC(=O)O…
LKM RCSB PDB P14900 486.5 Da LogP 3.03 TPSA 153.8 ✓ Ro5 ✓ Clean c1cc(c(cc1C#N)F)COc2ccc3cc(ccc3c2)S(=O)(=O)NC(C…
MLI RCSB PDB P14900 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
N04 RCSB PDB P14900 484.5 Da LogP 2.64 TPSA 159.1 ✓ Ro5 ✓ Clean c1cc(cc(c1)C(=O)N[C@H](CCC(=O)O)C(=O)O)COc2cccc…
N21 RCSB PDB P14900 520.5 Da LogP 2.19 TPSA 176.2 1 viol. ✓ Clean c1cc(ccc1COc2ccc(cc2)\C=C/3\C(=O)NC(=O)S3)S(=O)…
T04 RCSB PDB P14900 517.6 Da LogP 2.97 TPSA 144.8 1 viol. Alert c1cc(ccc1\C=C/2\C(=O)NC(=S)S2)NCc3ccc(c(c3)C(=O…
T26 RCSB PDB P14900 499.6 Da LogP 2.84 TPSA 144.8 ✓ Ro5 Alert c1cc(cc(c1)NCc2ccc(cc2)\C=C/3\C(=O)NC(=S)S3)C(=…
UAG RCSB PDB P14900 879.6 Da LogP -5.30 TPSA 427.7 3 viol. ✓ Clean C[C@@H](C(=O)N[C@H](CCC(=O)O)C(=O)O)NC(=O)[C@@H…
UD1 RCSB PDB P65473 607.4 Da LogP -4.65 TPSA 305.9 3 viol. ✓ Clean CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1O[P@@]…
UMA RCSB PDB P45066 750.5 Da LogP -4.65 TPSA 361.3 3 viol. ✓ Clean C[C@@H](C(=O)O)NC(=O)[C@@H](C)O[C@@H]1[C@H]([C@…
UXP RCSB PDB Q9HW02 354.4 Da LogP 2.05 TPSA 118.6 ✓ Ro5 ✓ Clean c1c([nH]nc1Nc2c3c[nH]nc3nc(n2)N4CCCC[C@@H]4CO)C…
UYD RCSB PDB Q9HW02 406.5 Da LogP 3.27 TPSA 116.6 ✓ Ro5 ✓ Clean CC(C)(C)c1cc(nn1C)Nc2c3cn[nH]c3nc(n2)N[C@@H](CO…
VSV RCSB PDB P14900 483.5 Da LogP 2.67 TPSA 161.9 ✓ Ro5 ✓ Clean c1cc(cc(c1)C(=O)N[C@H](CCC(=O)O)C(=O)O)CNc2ccc(…

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.