Protein target profile

KP13_03773

Imidazole glycerol phosphate synthase subunit

Genome: KpKP13 Gene: hisF AHE43690.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQM9

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Length 241

Pocket druggability 0.997

Direct ligand evidence 0 57 total records

Functional annotation 1 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

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 1.00, P2Rank 0.98). Use the 3D pocket comparison to verify whether they identify the same site. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Strong predicted binding pocket FPocket selected-pocket score 1.00. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.98. 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: No hit
Gut microbiome similarity: 3.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 41.322 Higher values support similarity to known essential genes.
DEG E-value: 2.28e-59 Smaller values mean stronger essential-gene similarity.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 90.2 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 0.997

Structure A0A0H3GQM9

Pocket Pocket 1

P2Rank 0.981

Structure A0A0H3GQM9

Pocket Pocket 1

ColabFold model

FPocket 0.889 · Pocket 1

P2Rank 0.993 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 181 / 4744 genomes with a hit

Prevalence 3.8%

Cross-references

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

Sequence

UniProt A0A0H3GQM9

Sequence

Primary amino-acid sequence viewer.

MKGVQFRNHEIIGDIVPLAKRYADEGADELVFYDITASSDGRVVDKSWVSRVAEVIDIPFCVAGGIKSLEDAAQILSFGADKISINSPALADPTLITRLADRFGVQCIVVGIDTWFDAETGKYHVNQYTGDESRTRVTQWETLDWVEEVQKRGAGEIVLNMMNQDGVRNGYDLKQLAKVRAVCHVPLIASGGAGTMEHFLEAFRDADVDGALAASVFHKQIINIGELKAYLAAQGVEIRVC

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

4.3.2.10

Gene Ontology (GO)

GO:0000105 The chemical reactions and pathways resulting in the formation of L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
GO:0000107 Catalysis of the reaction: phosphoribulosylformimino-AICAR-P + L-glutamine = D-erythro-imidazole-glycerol-phosphate + aminoimidazole carboxamide ribonucleotide + L-glutamate + 2 H+.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
1	241	Gene3D	G3DSA:3.20.20.70	Aldolase class I
1	241	InterPro	IPR013785	Aldolase-type TIM barrel
2	234	CDD	cd04731	HisF
2	234	InterPro	IPR004651	Histidine biosynthesis, HisF
1	240	FunFam	G3DSA:3.20.20.70:FF:000006	Imidazole glycerol phosphate synthase subunit HisF
2	239	NCBIfam	TIGR00735	imidazole glycerol phosphate synthase subunit HisF
2	239	InterPro	IPR004651	Histidine biosynthesis, HisF
2	222	Pfam	PF00977	Histidine biosynthesis protein
2	222	InterPro	IPR006062	Histidine biosynthesis protein
1	240	PANTHER	PTHR21235	IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISF/H IGP SYNTHASE SUBUNIT HISF/H
2	240	SUPERFAMILY	SSF51366	Ribulose-phoshate binding barrel
2	240	InterPro	IPR011060	Ribulose-phosphate binding barrel

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

0.997

Likely same site as P2Rank 1 3.0 Å 38 shared residues 95% 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

0.981

Likely same site as FPocket 1 3.0 Å 38 shared residues 95% of smaller site

Show in viewer

Surrounding area

Site 2 P2Rank #2

0.082

Show in viewer

Surrounding area

Residue sets

UniProt: Active site:11-11

UniProt: Active site:130-130

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_A0A0H3GQM9	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_03773	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.

57 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 7 records from similar proteins

Structural ligands 7 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

0VR PDB via homolog 351.2 Da · LogP -1.01 · TPSA 176.8 Open detail RCSB PDB

137 PDB via homolog Detail RCSB PDB

1PR PDB via homolog Detail RCSB PDB

2ER PDB via homolog Detail RCSB PDB

AMZ 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
0VR RCSB PDB	4EWN	Q9X0C6	351.2 Da LogP -1.01 TPSA 176.8	1 viol.	✓ Clean	`c1ccc(c(c1)C(=O)O)NC[C@@H]([C@@H]([C@@H](COP(=O…`
137 RCSB PDB	2Y85	P9WMM5	351.2 Da LogP -1.01 TPSA 176.8	1 viol.	✓ Clean	`c1ccc(c(c1)C(=O)O)NC[C@H]([C@@H]([C@@H](COP(=O)…`
1PR RCSB PDB	1OX5	P33734	581.4 Da LogP -5.14 TPSA 328.9	3 viol.	✓ Clean	`c1nc(c(n1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O…`
2ER RCSB PDB	5AB3	P10372	577.3 Da LogP -4.45 TPSA 326.0	3 viol.	✓ Clean	`c1nc(c(n1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O…`
AMZ RCSB PDB	5DN1	P16250	338.2 Da LogP -2.71 TPSA 203.4	1 viol.	✓ Clean	`c1nc(c(n1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O…`
GUO RCSB PDB	5A5W	P10372	577.3 Da LogP -4.48 TPSA 318.2	3 viol.	✓ Clean	`c1nc(c(n1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O…`
POP RCSB PDB	1JVN	P33734	176.0 Da LogP -2.08 TPSA 129.9	✓ Ro5	✓ Clean	`O[P@@](=O)([O-])O[P@@](=O)(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
ZINC4096530 ZINC	0.667	366.2 Da LogP -2.72 TPSA 206.5	1 viol.	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC2390999 ZINC	0.655	275.3 Da LogP -1.99 TPSA 172.8	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC103317774 ZINC	0.639	338.2 Da LogP -2.71 TPSA 203.4	1 viol.	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC12501010 ZINC	0.639	338.2 Da LogP -2.71 TPSA 203.4	1 viol.	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC22048479 ZINC	0.639	338.2 Da LogP -2.71 TPSA 203.4	1 viol.	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC3869390 ZINC	0.639	338.2 Da LogP -2.71 TPSA 203.4	1 viol.	✓ Clean	`NC(=O)c1ncn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869391 ZINC	0.639	338.2 Da LogP -2.71 TPSA 203.4	1 viol.	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC3869392 ZINC	0.639	338.2 Da LogP -2.71 TPSA 203.4	1 viol.	✓ Clean	`NC(=O)c1ncn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869393 ZINC	0.639	338.2 Da LogP -2.71 TPSA 203.4	1 viol.	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC4096500 ZINC	0.639	338.2 Da LogP -2.71 TPSA 203.4	1 viol.	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3055005 ZINC	0.591	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O`
ZINC3055007 ZINC	0.591	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055010 ZINC	0.591	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC2391099 ZINC	0.586	274.3 Da LogP -2.59 TPSA 178.6	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](N)C(=O)N[C@@H](CCC(N)=O)C(=O)O`
ZINC2556600 ZINC	0.567	217.2 Da LogP -1.83 TPSA 135.5	✓ Ro5	✓ Clean	`C[C@H](NC(=O)[C@@H](N)CCC(N)=O)C(=O)O`
ZINC1555366 ZINC	0.565	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1555367 ZINC	0.565	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1555369 ZINC	0.565	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720127 ZINC	0.565	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1720128 ZINC	0.565	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720130 ZINC	0.565	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC4096533 ZINC	0.563	339.2 Da LogP -2.11 TPSA 197.6	1 viol.	✓ Clean	`Nc1c(C(=O)O)ncn1[C@@H]1O[C@H](COP(=O)(O)O)[C@@H…`
ZINC88466335 ZINC	0.563	338.2 Da LogP -2.71 TPSA 203.4	1 viol.	✓ Clean	`NC(=O)c1c(N)ncn1[C@@H]1O[C@H](COP(=O)(O)O)[C@@H…`
ZINC1581634 ZINC	0.552	203.2 Da LogP -2.22 TPSA 135.5	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](N)C(=O)NCC(=O)O`
ZINC5500823 ZINC	0.552	203.2 Da LogP -2.22 TPSA 135.5	✓ Ro5	✓ Clean	`NC(=O)CC[C@@H](N)C(=O)NCC(=O)O`
ZINC4096553 ZINC	0.535	454.3 Da LogP -3.15 TPSA 264.0	2 viol.	✓ Clean	`Nc1c(C(=O)N[C@@H](CC(=O)O)C(=O)O)ncn1[C@@H]1O[C…`
ZINC12402859 ZINC	0.531	324.2 Da LogP -2.89 TPSA 190.2	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC12501004 ZINC	0.531	324.2 Da LogP -2.89 TPSA 190.2	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC1562441 ZINC	0.531	324.2 Da LogP -2.89 TPSA 190.2	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC22066422 ZINC	0.531	324.2 Da LogP -2.89 TPSA 190.2	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC22066425 ZINC	0.531	324.2 Da LogP -2.89 TPSA 190.2	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC2560992 ZINC	0.531	275.3 Da LogP -1.99 TPSA 172.8	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](N)C(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC5372441 ZINC	0.531	324.2 Da LogP -2.89 TPSA 190.2	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC5372445 ZINC	0.531	324.2 Da LogP -2.89 TPSA 190.2	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC5372450 ZINC	0.531	324.2 Da LogP -2.89 TPSA 190.2	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC1703514 ZINC	0.520	285.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`COC(=O)c1ccccc1NC[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC4824070 ZINC	0.520	285.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`COC(=O)c1ccccc1NC[C@H](O)[C@H](O)[C@H](O)CO`
ZINC4824072 ZINC	0.520	285.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`COC(=O)c1ccccc1NC[C@H](O)[C@@H](O)[C@H](O)CO`
ZINC4824074 ZINC	0.520	285.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`COC(=O)c1ccccc1NC[C@@H](O)[C@@H](O)[C@H](O)CO`
ZINC2106542 ZINC	0.519	245.3 Da LogP 1.99 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCCCCCC(=O)O)C(=O)O`
ZINC2106543 ZINC	0.519	245.3 Da LogP 1.99 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCCCCCC(=O)O)C(=O)O`
ZINC2108713 ZINC	0.519	217.3 Da LogP 1.21 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCCCC(=O)O)C(=O)O`
ZINC2108714 ZINC	0.519	217.3 Da LogP 1.21 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCCCC(=O)O)C(=O)O`
ZINC1529737 ZINC	0.517	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC1576202 ZINC	0.517	204.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)NCC(=O)O)C(=O)O`
ZINC2384790 ZINC	0.517	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC2560745 ZINC	0.517	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)O`
ZINC3995565 ZINC	0.517	204.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)NCC(=O)O)C(=O)O`
ZINC53683597 ZINC	0.517	202.3 Da LogP -0.08 TPSA 95.4	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@@H](N)CCC(N)=O`
ZINC56963153 ZINC	0.517	202.3 Da LogP -0.08 TPSA 95.4	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@H](N)CCC(N)=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.