Protein profile

KP13_03772

Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase

Genome: KpKP13

Gene: AHE43691.1 hisA Structure source: AlphaFold + ColabFold UniProt A0A0H3H0J1

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Amino acids 245

Annotations 5

Features 15

PDB binders 6

Druggability 0.968

Overview

Basic information about this protein and its source genome.

Accession: KP13_03772
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43691.1 hisA
Status: annotated
Amino acids: 245
Structure source: AlphaFold + ColabFold

5.3.1.16

GO:0000105 The chemical reactions and pathways resulting in the formation of L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid. GO:0003949 Catalysis of the reaction: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0000162 The chemical reactions and pathways resulting in the formation of L-tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; L-tryptophan is synthesized from chorismate via anthranilate.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 63.673
DEG E-value: 2.98e-114
Localization: Cytoplasmic
ColabFold pLDDT: 95.7

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.968

Structure A0A0H3H0J1

Pocket Pocket 1

P2Rank 0.991

Structure A0A0H3H0J1

Pocket Pocket 1

ColabFold model

FPocket 0.823 · Pocket 1

P2Rank 0.988 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 173 / 4744 genomes with a hit

Normalized 0.036

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

5.3.1.16

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:0003949 Catalysis of the reaction: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide = 5-[(5-phospho-1-deoxy-D-ribulos-1-ylimino)methylamino]-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0000162 The chemical reactions and pathways resulting in the formation of L-tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; L-tryptophan is synthesized from chorismate via anthranilate.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
1	241	Hamap	MF_01014	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase [hisA].
1	241	InterPro	IPR023016	HisA/PriA, bacterial-type
1	233	Pfam	PF00977	Histidine biosynthesis protein
1	233	InterPro	IPR006062	Histidine biosynthesis protein
2	242	PANTHER	PTHR43090	1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO)METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE
2	242	InterPro	IPR044524	Histidine biosynthesis, HisA-like
1	244	FunFam	G3DSA:3.20.20.70:FF:000009	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
1	243	SUPERFAMILY	SSF51366	Ribulose-phoshate binding barrel
1	243	InterPro	IPR011060	Ribulose-phosphate binding barrel
2	238	NCBIfam	TIGR00007	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
2	238	InterPro	IPR006063	HisA, bacterial-type
1	240	CDD	cd04732	HisA
1	240	InterPro	IPR023016	HisA/PriA, bacterial-type
1	245	Gene3D	G3DSA:3.20.20.70	Aldolase class I
1	245	InterPro	IPR013785	Aldolase-type TIM barrel

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3H0J1	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03772	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
1				0.968

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				54.35	0.984
2				1.37	0.016

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
1				0.823

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				48.84	0.978
2				1.53	0.022

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.

56 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, 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
137	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	3ZS4	P9WMM5	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	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	4TX9	B5I4P8	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…`
CXS	4X2R	C0W7K4	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCCS(=O)(=O)O`
GUO	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…`

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
ZINC2004372	1.000	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC3869392	1.000	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)…`
ZINC38364153	0.926	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
ZINC1710230	0.786	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC4096530	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)…`
ZINC5188799	0.630	280.5 Da LogP 4.39 TPSA 24.1	✓ Ro5	✓ Clean	`C(CCCNC1CCCCC1)CCNC1CCCCC1`
ZINC5606507	0.614	363.2 Da LogP -2.62 TPSA 200.1	✓ Ro5	✓ Clean	`Nc1c2ncn([C@H]3O[C@@H](COP(=O)(O)O)[C@@H](O)[C@…`
ZINC13518964	0.607	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.607	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1560705	0.607	347.2 Da LogP -1.91 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@H…`
ZINC1571045	0.607	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.607	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.607	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.607	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.607	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.607	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.607	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.607	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.607	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.607	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC5250137	0.607	347.2 Da LogP -1.91 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@H]…`
ZINC5250138	0.607	347.2 Da LogP -1.91 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@@H…`
ZINC5250139	0.607	347.2 Da LogP -1.91 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@@…`
ZINC8613167	0.607	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC12501413	0.593	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC12958448	0.593	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC1532555	0.593	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC16546189	0.593	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC2159505	0.593	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3073318	0.593	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869963	0.593	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869965	0.593	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC9334496	0.593	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC103317774	0.582	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	0.582	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	0.582	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	0.582	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	0.582	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	0.582	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	0.582	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)…`
ZINC11616626	0.576	365.2 Da LogP -1.72 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H…`
ZINC1555157	0.576	365.2 Da LogP -1.72 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H…`
ZINC33902473	0.576	365.2 Da LogP -1.72 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@…`
ZINC3830848	0.576	365.2 Da LogP -1.72 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@…`
ZINC3830849	0.576	365.2 Da LogP -1.72 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@…`
ZINC3830850	0.576	365.2 Da LogP -1.72 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@…`
ZINC3830851	0.576	365.2 Da LogP -1.72 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@…`
ZINC3927870	0.576	365.2 Da LogP -1.72 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@…`
ZINC64479802	0.576	365.2 Da LogP -1.72 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H…`
ZINC80452830	0.576	365.2 Da LogP -1.72 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1nc(F)nc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H…`

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.