Protein profile

VK055_5042

hisB

Genome: KpATCC43816

Gene: AIK83568.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GV71

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Amino acids 355

Annotations 6

Features 38

PDB binders 5

Druggability 0.318

Overview

Basic information about this protein and its source genome.

Accession: VK055_5042
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK83568.1
Status: annotated
Amino acids: 355
Structure source: AlphaFold + ColabFold

GO:0000105 The chemical reactions and pathways resulting in the formation of L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid. GO:0016791 Catalysis of the hydrolysis of a phosphoric monoester, releasing a phosphate. GO:0004401 Catalysis of the reaction: L-histidinol phosphate + H2O = L-histidinol + phosphate. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0004424 Catalysis of the reaction: D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O. GO:0046872 Binding to a metal ion.

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 (%): 60.773
DEG E-value: 3.3800000000000003e-166
Localization: Cytoplasmic
ColabFold pLDDT: 94.08

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 0.318

Structure A0A0H3GV71

Pocket Pocket 4

P2Rank 0.13

Structure A0A0H3GV71

Pocket Pocket 1

ColabFold model

FPocket 0.349 · Pocket 20

P2Rank 0.075 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 181 / 4744 genomes with a hit

Normalized 0.038

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

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:0016791 Catalysis of the hydrolysis of a phosphoric monoester, releasing a phosphate.
GO:0004401 Catalysis of the reaction: L-histidinol phosphate + H2O = L-histidinol + phosphate.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0004424 Catalysis of the reaction: D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O.
GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

38 records

Show feature table

Start	End	DB	Term	Name
196	337	Pfam	PF00475	Imidazoleglycerol-phosphate dehydratase
196	337	InterPro	IPR000807	Imidazoleglycerol-phosphate dehydratase
160	355	PANTHER	PTHR23133	IMIDAZOLEGLYCEROL-PHOSPHATE DEHYDRATASE HIS7
160	355	InterPro	IPR000807	Imidazoleglycerol-phosphate dehydratase
319	331	ProSitePatterns	PS00955	Imidazoleglycerol-phosphate dehydratase signature 2.
319	331	InterPro	IPR020565	Imidazoleglycerol-phosphate dehydratase, conserved site
3	162	NCBIfam	TIGR01261	HisB N-terminal histidinol-phosphatase domain
3	162	InterPro	IPR005954	Histidine biosynthesis bifunctional protein, N-terminal histidinol-phosphatase domain
8	132	Pfam	PF08645	Polynucleotide kinase 3 phosphatase
8	132	InterPro	IPR013954	Polynucleotide kinase 3 phosphatase
4	148	CDD	cd07503	HAD_HisB-N
2	355	Hamap	MF_01022	Histidine biosynthesis bifunctional protein HisB [hisB].
2	355	InterPro	IPR020566	Histidine biosynthesis bifunctional protein HisB
4	147	NCBIfam	TIGR01662	HAD-IIIA family hydrolase
4	147	InterPro	IPR006549	HAD-superfamily hydrolase,subfamily IIIA
5	144	NCBIfam	TIGR01656	histidinol-phosphate phosphatase domain
5	144	InterPro	IPR006543	Histidinol-phosphate phosphatase
1	162	FunFam	G3DSA:3.40.50.1000:FF:000061	Histidine biosynthesis bifunctional protein HisB
162	254	Gene3D	G3DSA:3.30.230.40	Imidazole glycerol phosphate dehydratase; domain 1
162	254	InterPro	IPR038494	Imidazole glycerol phosphate dehydratase domain superfamily
169	355	CDD	cd07914	IGPD
169	355	InterPro	IPR000807	Imidazoleglycerol-phosphate dehydratase
167	355	Hamap	MF_00076	Imidazoleglycerol-phosphate dehydratase [hisB].
167	355	InterPro	IPR000807	Imidazoleglycerol-phosphate dehydratase
255	355	FunFam	G3DSA:3.30.230.40:FF:000001	Imidazoleglycerol-phosphate dehydratase HisB
226	239	ProSitePatterns	PS00954	Imidazoleglycerol-phosphate dehydratase signature 1.
226	239	InterPro	IPR020565	Imidazoleglycerol-phosphate dehydratase, conserved site
1	161	Gene3D	G3DSA:3.40.50.1000	-
1	161	InterPro	IPR023214	HAD superfamily
160	254	FunFam	G3DSA:3.30.230.40:FF:000003	Imidazoleglycerol-phosphate dehydratase HisB
167	251	SUPERFAMILY	SSF54211	Ribosomal protein S5 domain 2-like
167	251	InterPro	IPR020568	Ribosomal protein S5 domain 2-type fold
1	156	SUPERFAMILY	SSF56784	HAD-like
1	156	InterPro	IPR036412	HAD-like superfamily
255	355	Gene3D	G3DSA:3.30.230.40	Imidazole glycerol phosphate dehydratase; domain 1
255	355	InterPro	IPR038494	Imidazole glycerol phosphate dehydratase domain superfamily
252	342	SUPERFAMILY	SSF54211	Ribosomal protein S5 domain 2-like
252	342	InterPro	IPR020568	Ribosomal protein S5 domain 2-type fold

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_A0A0H3GV71	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_5042	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
2				0.053
3				0.001
1				0.0
5				0.0

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				4.01	0.13
2				1.17	0.009

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
20				0.349
5				0.01
1				0.009
2				0.0

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				2.93	0.075

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.

54 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
5DL	5EKW	O23346	207.1 Da LogP -1.18 TPSA 108.5	✓ Ro5	✓ Clean	`c1ncn(n1)C[C@@H](CP(=O)(O)O)O`
5LD	6FWH	L8H477	207.1 Da LogP -1.18 TPSA 108.5	✓ Ro5	✓ Clean	`c1ncn(n1)C[C@H](CP(=O)(O)O)O`
EMC	1RHY	P0CO22	229.7 Da LogP 0.97 TPSA 0.0	✓ Ro5	✓ Clean	`CC[Hg+]`
IYP	4MU4	O23346	238.1 Da LogP -1.09 TPSA 135.9	✓ Ro5	✓ Clean	`c1c([nH]cn1)[C@@H]([C@@H](COP(=O)(O)O)O)O`
TRI	4MU0	O23346	69.1 Da LogP -0.20 TPSA 41.6	✓ Ro5	✓ Clean	`c1[nH]cnn1`

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL50542	P0CO23	9.22	207.1 Da LogP -1.18 TPSA 108.5	✓ Ro5	✓ Clean	`O=P(O)(O)CC(O)Cn1cncn1`
CHEMBL63035	P0CO23	7.82	206.1 Da LogP -1.22 TPSA 114.3	✓ Ro5	✓ Clean	`NC(Cn1cncn1)CP(=O)(O)O`
CHEMBL60155	P0CO23	7.10	340.3 Da LogP 0.02 TPSA 126.6	✓ Ro5	✓ Clean	`O=C(COc1ccccc1)NC(Cn1cncn1)CP(=O)(O)O`
CHEMBL303762	P0CO23	6.64	264.2 Da LogP -2.07 TPSA 137.6	✓ Ro5	✓ Clean	`O=C(CO)NC(Cn1cncn1)CP(=O)(O)O`
CHEMBL418642	P0CO23	6.64	354.3 Da LogP 0.41 TPSA 126.6	✓ Ro5	✓ Clean	`CC(Oc1ccccc1)C(=O)NC(Cn1cncn1)CP(=O)(O)O`
CHEMBL62933	P0CO23	6.60	356.3 Da LogP 0.73 TPSA 117.3	✓ Ro5	✓ Clean	`O=C(CSc1ccccc1)NC(Cn1cncn1)CP(=O)(O)O`
CHEMBL423851	P0CO23	6.57	338.3 Da LogP 0.57 TPSA 117.3	✓ Ro5	✓ Clean	`O=C(CCc1ccccc1)NC(Cn1cncn1)CP(=O)(O)O`
CHEMBL64769	P0CO23	6.47	304.3 Da LogP 0.52 TPSA 117.3	✓ Ro5	✓ Clean	`CCCCCC(=O)NC(Cn1cncn1)CP(=O)(O)O`
CHEMBL66416	P0CO23	6.47	324.3 Da LogP 0.18 TPSA 117.3	✓ Ro5	✓ Clean	`O=C(Cc1ccccc1)NC(Cn1cncn1)CP(=O)(O)O`
CHEMBL304038	P0CO23	6.26	374.7 Da LogP 0.67 TPSA 126.6	✓ Ro5	✓ Clean	`O=C(COc1ccc(Cl)cc1)NC(Cn1cncn1)CP(=O)(O)O`
CHEMBL63147	P0CO23	6.25	330.3 Da LogP 0.24 TPSA 117.3	✓ Ro5	✓ Clean	`O=C(Cc1cccs1)NC(Cn1cncn1)CP(=O)(O)O`
CHEMBL65577	P0CO23	6.16	334.3 Da LogP -0.72 TPSA 143.6	✓ Ro5	✓ Clean	`COC(=O)CCCC(=O)NC(Cn1cncn1)CP(=O)(O)O`
CHEMBL293612	P0CO23	6.10	248.2 Da LogP -1.04 TPSA 117.3	✓ Ro5	✓ Clean	`CC(=O)NC(Cn1cncn1)CP(=O)(O)O`
CHEMBL294077	P0CO23	6.10	380.4 Da LogP 0.92 TPSA 117.3	✓ Ro5	✓ Clean	`CC1(CCC(=O)NC(Cn2cncn2)CP(=O)(O)O)SCCS1`
CHEMBL294774	P0CO23	6.06	330.3 Da LogP 0.91 TPSA 117.3	✓ Ro5	✓ Clean	`O=C(CCC1CCCC1)NC(Cn1cncn1)CP(=O)(O)O`

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
ZINC3869788	1.000	238.1 Da LogP -1.09 TPSA 135.9	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)c1cnc[nH]1`
ZINC585150369	0.576	304.3 Da LogP 0.88 TPSA 78.3	✓ Ro5	✓ Clean	`C[C@@H](Oc1ccccc1)C(=O)NCCOCCn1cncn1`
ZINC585150371	0.576	304.3 Da LogP 0.88 TPSA 78.3	✓ Ro5	✓ Clean	`C[C@H](Oc1ccccc1)C(=O)NCCOCCn1cncn1`
ZINC58481767	0.567	336.4 Da LogP 2.41 TPSA 69.0	✓ Ro5	✓ Clean	`C[C@H](Oc1ccccc1)C(=O)NCc1ccc(Cn2cncn2)cc1`
ZINC58481768	0.567	336.4 Da LogP 2.41 TPSA 69.0	✓ Ro5	✓ Clean	`C[C@@H](Oc1ccccc1)C(=O)NCc1ccc(Cn2cncn2)cc1`
ZINC32904430	0.561	312.4 Da LogP 2.25 TPSA 59.8	✓ Ro5	✓ Clean	`O=C(Cc1cccs1)NCc1ccc(Cn2cncn2)cc1`
ZINC32818630	0.544	322.4 Da LogP 2.02 TPSA 69.0	✓ Ro5	✓ Clean	`O=C(COc1ccccc1)NCc1ccccc1Cn1cncn1`
ZINC585150491	0.525	290.3 Da LogP 0.49 TPSA 78.3	✓ Ro5	✓ Clean	`O=C(COc1ccccc1)NCCOCCn1cncn1`
ZINC767103616	0.525	288.4 Da LogP 0.78 TPSA 80.0	✓ Ro5	✓ Clean	`O=C(CCCn1cncn1)N[C@@H](CO)Cc1ccccc1`
ZINC23950802	0.525	336.4 Da LogP 2.91 TPSA 69.0	✓ Ro5	✓ Clean	`C[C@@H](Oc1ccccc1)C(=O)N[C@H](C)c1ccc(-n2cncn2)…`
ZINC23950804	0.525	336.4 Da LogP 2.91 TPSA 69.0	✓ Ro5	✓ Clean	`C[C@H](NC(=O)[C@@H](C)Oc1ccccc1)c1ccc(-n2cncn2)…`
ZINC23950806	0.525	336.4 Da LogP 2.91 TPSA 69.0	✓ Ro5	✓ Clean	`C[C@H](Oc1ccccc1)C(=O)N[C@H](C)c1ccc(-n2cncn2)c…`
ZINC23950808	0.525	336.4 Da LogP 2.91 TPSA 69.0	✓ Ro5	✓ Clean	`C[C@H](Oc1ccccc1)C(=O)N[C@@H](C)c1ccc(-n2cncn2)…`
ZINC55968721	0.517	324.4 Da LogP 3.06 TPSA 59.8	✓ Ro5	✓ Clean	`O=C(CSc1ccccc1)Nc1ccccc1Cn1cncn1`
ZINC55968998	0.517	306.4 Da LogP 2.90 TPSA 59.8	✓ Ro5	✓ Clean	`O=C(CCc1ccccc1)Nc1ccccc1Cn1cncn1`
ZINC71185604	0.517	264.4 Da LogP 1.48 TPSA 59.8	✓ Ro5	✓ Clean	`C[C@@H](Cc1cccs1)NC(=O)CCn1cncn1`
ZINC71185605	0.517	264.4 Da LogP 1.48 TPSA 59.8	✓ Ro5	✓ Clean	`C[C@H](Cc1cccs1)NC(=O)CCn1cncn1`
ZINC23404910	0.509	236.3 Da LogP 1.05 TPSA 59.8	✓ Ro5	✓ Clean	`O=C(CCn1cncn1)NCc1cccs1`
ZINC12974659	0.508	322.4 Da LogP 2.52 TPSA 69.0	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)COc1ccccc1)c1ccc(-n2cncn2)cc1`
ZINC12974661	0.508	322.4 Da LogP 2.52 TPSA 69.0	✓ Ro5	✓ Clean	`C[C@H](NC(=O)COc1ccccc1)c1ccc(-n2cncn2)cc1`
ZINC25691862	0.508	312.4 Da LogP 2.75 TPSA 59.8	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)Cc1cccs1)c1ccc(-n2cncn2)cc1`
ZINC25691866	0.508	312.4 Da LogP 2.75 TPSA 59.8	✓ Ro5	✓ Clean	`C[C@H](NC(=O)Cc1cccs1)c1ccc(-n2cncn2)cc1`
ZINC43246290	0.508	338.4 Da LogP 2.37 TPSA 78.3	✓ Ro5	✓ Clean	`O=C(COc1ccccc1)Nc1cccc(OCCn2cncn2)c1`
ZINC952964804	0.508	286.3 Da LogP 1.20 TPSA 60.2	✓ Ro5	✓ Clean	`C[C@@H](Oc1ccccc1)C(=O)N1CC(Cn2cncn2)C1`
ZINC952964814	0.508	286.3 Da LogP 1.20 TPSA 60.2	✓ Ro5	✓ Clean	`C[C@H](Oc1ccccc1)C(=O)N1CC(Cn2cncn2)C1`
ZINC222782383	0.500	335.4 Da LogP 2.55 TPSA 72.7	✓ Ro5	✓ Clean	`O=C(CCc1cccnc1)N[C@@H](CCn1cncn1)c1ccccc1`
ZINC222782450	0.500	335.4 Da LogP 2.55 TPSA 72.7	✓ Ro5	✓ Clean	`O=C(CCc1cccnc1)N[C@H](CCn1cncn1)c1ccccc1`
ZINC23735477	0.500	244.3 Da LogP 1.03 TPSA 59.8	✓ Ro5	✓ Clean	`O=C(CCn1cncn1)NCCc1ccccc1`
ZINC31778	0.500	235.3 Da LogP 2.76 TPSA 38.3	✓ Ro5	✓ Clean	`CCC(CC)NC(=O)[C@@H](C)Oc1ccccc1`
ZINC42501941	0.500	249.3 Da LogP 1.69 TPSA 46.9	✓ Ro5	✓ Clean	`C[C@@H](Cn1cccn1)NC(=O)Cc1cccs1`
ZINC42501944	0.500	249.3 Da LogP 1.69 TPSA 46.9	✓ Ro5	✓ Clean	`C[C@H](Cn1cccn1)NC(=O)Cc1cccs1`
ZINC4675339	0.500	235.3 Da LogP 2.76 TPSA 38.3	✓ Ro5	✓ Clean	`CCC(CC)NC(=O)[C@H](C)Oc1ccccc1`
ZINC67872208	0.500	263.4 Da LogP 2.08 TPSA 46.9	✓ Ro5	✓ Clean	`CC[C@@H](Cn1ccnc1)NC(=O)Cc1cccs1`
ZINC67872210	0.500	263.4 Da LogP 2.08 TPSA 46.9	✓ Ro5	✓ Clean	`CC[C@H](Cn1ccnc1)NC(=O)Cc1cccs1`

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.