Protein target profile

KP13_05272

putative isomerase

Genome: KpKP13 Gene: AHE44679.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GN46

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Length 264

Pocket druggability 0.532

Direct ligand evidence 0 55 total records

Functional annotation 0 EC 4 GO

Target summary

Promising target candidate with multiple supporting evidence streams.

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

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.53. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.82. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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: Hit
Human identity (%): 36.364 Lower values reduce human off-target concern.
Human E-value: 1.06e-42
Gut microbiome similarity: 1.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 96.97 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 0.532

Structure A0A0H3GN46

Pocket Pocket 12

P2Rank 0.816

Structure A0A0H3GN46

Pocket Pocket 1

ColabFold model

FPocket 0.307 · Pocket 13

P2Rank 0.794 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 58 / 4744 genomes with a hit

Prevalence 1.2%

Cross-references

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

Sequence

UniProt A0A0H3GN46

Sequence

Primary amino-acid sequence viewer.

MQEIQFYLVDAFSDKNFGGNAAAVCPLSEWLADDVLLKMAQQHNQSETAFFVRTDEGYELRWFTTLAEINLCGHATLAAAHVIFEYLDHPSATILFSTRFVGELRVTRNGDWLTLDFPAWSTSPVENPPADLLTGLGLEAAVEVREGRDYLVVLADRQQVEAVRPDMARLRTLGKMICVSAPDEEYDFVSRFFCPGEGVPEDPVTGSAHSMLIPWWGEKLGKTTMMARQISARGGDLRCQWQGDRVLISGQATTYMRGTVYLRG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

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:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0016853 Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

11 records

Show feature table

Start	End	DB	Term	Name
3	235	NCBIfam	TIGR00654	PhzF family phenazine biosynthesis isomerase
3	235	InterPro	IPR003719	Phenazine biosynthesis PhzF-like
5	261	PANTHER	PTHR13774	PHENAZINE BIOSYNTHESIS PROTEIN
5	261	InterPro	IPR003719	Phenazine biosynthesis PhzF-like
9	258	Pfam	PF02567	Phenazine biosynthesis-like protein
9	258	InterPro	IPR003719	Phenazine biosynthesis PhzF-like
3	262	SUPERFAMILY	SSF54506	Diaminopimelate epimerase-like
1	262	PIRSF	PIRSF016184	Ismrse_PhzF
1	262	InterPro	IPR003719	Phenazine biosynthesis PhzF-like
119	250	Gene3D	G3DSA:3.10.310.10	Diaminopimelate Epimerase; Chain A, domain 1
6	254	Gene3D	G3DSA:3.10.310.10	Diaminopimelate Epimerase; Chain A, domain 1

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 #12

0.532

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Surrounding area

Site 2 FPocket #15

0.241

Likely same site as P2Rank 1 1.7 Å 19 shared residues 100% of smaller site

Unusual size

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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.816

Likely same site as FPocket 15 1.7 Å 19 shared residues 100% of smaller site

Show in viewer

Surrounding area

Residue sets

UniProt: Active site:47-47

Binding pockets · FPocket

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

Site 1 FPocket #13

0.307

Show in viewer

Surrounding area

Site 2 FPocket #3

0.239

Likely same site as P2Rank 1 3.6 Å 17 shared residues 81% of smaller site

Unusual size

Show in viewer

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_A0A0H3GN46	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_05272	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.

55 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 5 records from similar proteins

Structural ligands 5 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

3HA PDB via homolog 153.1 Da · LogP 0.67 · TPSA 83.5 Open detail RCSB PDB

BTB PDB via homolog Detail RCSB PDB

HHA PDB via homolog Detail RCSB PDB

SIN PDB via homolog Detail RCSB PDB

W81 PDB via homolog Detail RCSB PDB

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
3HA RCSB PDB	1U1W	Q51792	153.1 Da LogP 0.67 TPSA 83.5	✓ Ro5	✓ Clean	`c1cc(c(c(c1)O)N)C(=O)O`
BTB RCSB PDB	4DUN	Q186X0	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`C(CO)N(CCO)C(CO)(CO)CO`
HHA RCSB PDB	1U1X	Q51792	155.2 Da LogP -0.74 TPSA 83.5	✓ Ro5	✓ Clean	`C1=C[C@@H]([C@H](C(=C1)C(=O)O)N)O`
SIN RCSB PDB	3EDN	A0A6L8PH16	118.1 Da LogP -0.06 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)O`
W81 RCSB PDB	5IWE	Q51792	183.2 Da LogP -1.75 TPSA 77.0	✓ Ro5	✓ Clean	`CCO[C@@H]1C=CC=C([C@H]1[NH3+])C(=O)[O-]`

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
ZINC1615342 ZINC	1.000	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN(CCO)C(CO)(CO)CO`
ZINC1703679 ZINC	0.630	216.0 Da LogP 1.73 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1c(Br)cccc1C(=O)O`
ZINC1721751 ZINC	0.630	263.0 Da LogP 1.57 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1c(I)cccc1C(=O)O`
ZINC1529497 ZINC	0.615	230.3 Da LogP 3.06 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCC(=O)O`
ZINC1531045 ZINC	0.615	202.2 Da LogP 2.28 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)O`
ZINC1593115 ZINC	0.615	216.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCC(=O)O`
ZINC1700020 ZINC	0.615	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=O)O`
ZINC3860440 ZINC	0.615	258.4 Da LogP 3.84 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCC(=O)O`
ZINC3861298 ZINC	0.615	286.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCC(=O)O`
ZINC5113062 ZINC	0.615	272.4 Da LogP 4.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCC(=O)O`
ZINC1081205 ZINC	0.567	205.1 Da LogP 1.99 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1c(C(=O)O)cccc1C(F)(F)F`
ZINC1572706 ZINC	0.563	260.2 Da LogP -1.05 TPSA 132.8	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)NCCNC(=O)CCC(=O)O`
ZINC82369423 ZINC	0.556	217.0 Da LogP 1.85 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cccc(O)c1Br`
ZINC95713705 ZINC	0.556	264.0 Da LogP 1.70 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cccc(O)c1I`
ZINC3869266 ZINC	0.545	224.2 Da LogP -0.04 TPSA 126.6	✓ Ro5	✓ Clean	`Nc1c(O)cccc1C(=O)C[C@H](N)C(=O)O`
ZINC901507 ZINC	0.545	224.2 Da LogP -0.04 TPSA 126.6	✓ Ro5	✓ Clean	`Nc1c(O)cccc1C(=O)C[C@@H](N)C(=O)O`
ZINC1600331 ZINC	0.542	330.2 Da LogP 2.15 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)O)c1-c1c(C(=O)O)cccc1C(=O)O`
ZINC1703342 ZINC	0.533	202.2 Da LogP 1.07 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)CCCC(=O)O`
ZINC1728397 ZINC	0.533	233.2 Da LogP -0.29 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)CCN(CCC(=O)O)CCC(=O)O`
ZINC2508031 ZINC	0.533	230.3 Da LogP 1.85 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)CCCCC(=O)O`
ZINC2517013 ZINC	0.533	250.2 Da LogP 0.89 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)CCP(CCC(=O)O)CCC(=O)O`
ZINC1697439 ZINC	0.529	219.5 Da LogP 1.79 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)C(Cl)(Cl)Cl`
ZINC35465466 ZINC	0.529	244.3 Da LogP 2.24 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCC(=O)CCC(=O)O`
ZINC39208104 ZINC	0.529	262.2 Da LogP -0.20 TPSA 127.2	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)OCCOC(=O)CCC(=O)O`
ZINC27644343 ZINC	0.528	364.4 Da LogP 3.25 TPSA 139.0	✓ Ro5	✓ Clean	`Nc1c(O)ccc2c1Oc1c(ccc(O)c1N)C2c1ccccc1C(=O)O`
ZINC2334905 ZINC	0.522	261.4 Da LogP 1.10 TPSA 63.9	✓ Ro5	✓ Clean	`CC(C)CCN(CCC(C)C)C(CO)(CO)CO`
ZINC3159953 ZINC	0.522	261.4 Da LogP 1.38 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCN(CCCCC)C(CO)(CO)CO`
ZINC388710 ZINC	0.520	210.1 Da LogP 0.78 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)O)c1C(=O)O`
ZINC45070868 ZINC	0.520	216.2 Da LogP 2.24 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1cccc2c(C(=O)O)cccc12`
ZINC1715583 ZINC	0.519	225.2 Da LogP 0.36 TPSA 137.9	✓ Ro5	✓ Clean	`Nc1c(C(=O)O)ccc(C(=O)O)c1C(=O)O`
ZINC40564457 ZINC	0.517	263.0 Da LogP 1.57 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)O)c1I`
ZINC40564460 ZINC	0.517	216.0 Da LogP 1.73 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)O)c1Br`
ZINC13352595 ZINC	0.515	221.1 Da LogP 1.87 TPSA 72.5	✓ Ro5	✓ Clean	`Nc1c(OC(F)(F)F)cccc1C(=O)O`
ZINC77270957 ZINC	0.515	320.1 Da LogP 2.96 TPSA 80.4	✓ Ro5	Alert	`Nc1c(C(=O)O)cccc1C(=O)c1ccc(Br)cc1`
ZINC1542984448 ZINC	0.500	470.5 Da LogP 0.07 TPSA 148.4	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCOCCC(=O)O`
ZINC1586444 ZINC	0.500	210.2 Da LogP -0.65 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)CCS(=O)(=O)CCC(=O)O`
ZINC1753095 ZINC	0.500	238.3 Da LogP 1.40 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCSCCSCCC(=O)O`
ZINC22028383 ZINC	0.500	204.2 Da LogP -0.88 TPSA 98.7	✓ Ro5	✓ Clean	`O=C(O)CCNCCNCCC(=O)O`
ZINC22576322 ZINC	0.500	348.4 Da LogP -0.51 TPSA 155.7	✓ Ro5	✓ Clean	`O=C(O)CCN(CCC(=O)O)CCN(CCC(=O)O)CCC(=O)O`
ZINC26897400 ZINC	0.500	286.4 Da LogP 3.41 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCCC(=O)O`
ZINC35977596 ZINC	0.500	294.3 Da LogP 0.00 TPSA 111.5	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCC(=O)O`
ZINC38682833 ZINC	0.500	286.3 Da LogP -0.61 TPSA 115.2	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)N1CCN(C(=O)CCC(=O)O)CC1`
ZINC39383060 ZINC	0.500	206.2 Da LogP -0.03 TPSA 93.1	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCC(=O)O`
ZINC39427081 ZINC	0.500	250.2 Da LogP -0.01 TPSA 102.3	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCC(=O)O`
ZINC4181831 ZINC	0.500	232.2 Da LogP -0.01 TPSA 129.0	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)C(CC(=O)O)CC(=O)O`
ZINC4822898 ZINC	0.500	272.3 Da LogP 3.02 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCC(=O)O`
ZINC4822900 ZINC	0.500	300.4 Da LogP 3.80 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)CCCCCC(=O)O`
ZINC71257127 ZINC	0.500	426.5 Da LogP 0.05 TPSA 139.2	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCC(=O)O`
ZINC71257128 ZINC	0.500	338.4 Da LogP 0.02 TPSA 120.8	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCC(=O)O`
ZINC79016464 ZINC	0.500	382.4 Da LogP 0.04 TPSA 130.0	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCC(=O)O`

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.