Protein profile

PA4939

ATP phosphoribosyltransferase

Genome: NC_002516.2

Gene: hisZ PA4939 Structure source: AlphaFold UniProt Q9HUM5

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Amino acids 394

Annotations 5

Features 16

PDB binders 21

Druggability 0.503

Overview

Basic information about this protein and its source genome.

Accession: PA4939
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: hisZ PA4939
Status: annotated
Amino acids: 394
Structure source: AlphaFold

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0004821 Catalysis of the reaction: ATP + L-histidine + tRNA(His) = AMP + diphosphate + L-histidyl-tRNA(His). GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0006427 The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. The histidyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3''-OH group of a histidine-accetping tRNA. GO:0000105 The chemical reactions and pathways resulting in the formation of L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 24.425
Human E-value: 3.87e-11
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

Selected Druggability evidence

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 0.503

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0004821 Catalysis of the reaction: ATP + L-histidine + tRNA(His) = AMP + diphosphate + L-histidyl-tRNA(His).
GO:0003723 Binding to an RNA molecule or a portion thereof.
GO:0006427 The process of coupling histidine to histidyl-tRNA, catalyzed by histidyl-tRNA synthetase. The histidyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3''-OH group of a histidine-accetping tRNA.
GO:0000105 The chemical reactions and pathways resulting in the formation of L-histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
5	333	Gene3D	G3DSA:3.30.930.10	Bira Bifunctional Protein; Domain 2
5	333	InterPro	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
20	324	CDD	cd00773	HisRS-like_core
20	324	InterPro	IPR041715	Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain
5	333	FunFam	G3DSA:3.30.930.10:FF:000161	ATP phosphoribosyltransferase regulatory subunit
19	373	Hamap	MF_00125	ATP phosphoribosyltransferase regulatory subunit [hisZ].
19	373	InterPro	IPR004517	ATP phosphoribosyltransferase regulatory subunit
7	388	PIRSF	PIRSF001549	His-tRNA_synth
7	388	InterPro	IPR004516	Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit
10	329	PANTHER	PTHR11476	HISTIDYL-TRNA SYNTHETASE
12	321	Pfam	PF13393	Histidyl-tRNA synthetase
12	321	InterPro	IPR041715	Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain
15	324	NCBIfam	TIGR00443	ATP phosphoribosyltransferase regulatory subunit
15	324	InterPro	IPR004517	ATP phosphoribosyltransferase regulatory subunit
7	324	SUPERFAMILY	SSF55681	Class II aaRS and biotin synthetases
7	324	InterPro	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)

3D Structure

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

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Structural evidence

0 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA4939	AlphaFold	—	—	full sequence	—	Viewing

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				0.503
3				0.218

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.

72 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
0P6	4YRC	Q4DA54	160.2 Da LogP 1.52 TPSA 59.1	✓ Ro5	✓ Clean	`c1cc2ccc(nc2c(c1)O)N`
282	4YRM	Q4DA54	109.1 Da LogP 1.09 TPSA 22.1	✓ Ro5	✓ Clean	`COc1cccnc1`
4FS	4YPF	Q4DA54	144.2 Da LogP 1.82 TPSA 38.9	✓ Ro5	✓ Clean	`c1ccc2c(c1)cc(cn2)N`
4HR	4YRE	Q4DA54	187.0 Da LogP 1.94 TPSA 20.2	✓ Ro5	✓ Clean	`c1ccc(c(c1)CO)Br`
4HS	4YRF	Q4DA54	174.0 Da LogP 1.14 TPSA 32.9	✓ Ro5	✓ Clean	`C1=CC(=O)NC=C1Br`
4HU	4YRG	Q4DA54	188.0 Da LogP 1.34 TPSA 33.1	✓ Ro5	✓ Clean	`c1cc(nc(c1)Br)CO`
4JH	4YRI	Q4DA54	186.1 Da LogP 1.91 TPSA 26.0	✓ Ro5	✓ Clean	`c1cc(cc(c1)Br)CN`
4JJ	4YRJ	Q4DA54	142.6 Da LogP 1.50 TPSA 52.0	✓ Ro5	✓ Clean	`c1cc(c(cc1Cl)N)N`
4JL	4YRK	Q4DA54	142.6 Da LogP 1.83 TPSA 20.2	✓ Ro5	✓ Clean	`c1cc(ccc1CO)Cl`
4JM	4YRL	Q4DA54	139.2 Da LogP 1.99 TPSA 26.0	✓ Ro5	✓ Clean	`CSc1ccc(cc1)N`
4JN	4YRN	Q4DA54	173.0 Da LogP 1.43 TPSA 38.9	✓ Ro5	✓ Clean	`c1cc(ncc1N)Br`
4JO	4YRO	Q4DA54	187.0 Da LogP 1.73 TPSA 38.9	✓ Ro5	✓ Clean	`Cc1c(ccc(n1)N)Br`
4JQ	4YRQ	Q4DA54	161.2 Da LogP 1.38 TPSA 56.2	✓ Ro5	✓ Clean	`c1cc2c(cc1N)C=CC(=O)O2`
4JS	4YRS	Q4DA54	200.2 Da LogP 2.58 TPSA 42.0	✓ Ro5	✓ Clean	`CCC(=O)Nc1cc2ccccc2nc1`
5IQ	4YP0	Q4DA54	144.2 Da LogP 1.82 TPSA 38.9	✓ Ro5	✓ Clean	`c1cc2cnccc2c(c1)N`
691	4YRR	Q4DA54	186.2 Da LogP 2.19 TPSA 42.0	✓ Ro5	✓ Clean	`CC(=O)Nc1cc2ccccc2nc1`
781	4YRT	Q4DA54	215.3 Da LogP 2.89 TPSA 49.3	✓ Ro5	✓ Clean	`CCC(=O)Nc1ccc2c(c1)cccc2O`
HAM	3HRK	Q4DA54	484.4 Da LogP -3.37 TPSA 251.3	1 viol.	✓ Clean	`c1c(nc[nH]1)C[C@@H](C(=O)O[P@](=O)([O-])OC[C@@H…`
LMR	3RAC	C8WUX4	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@@H](C(=O)O)O)C(=O)O`
PZH	4YRP	Q4DA54	186.1 Da LogP 1.91 TPSA 26.0	✓ Ro5	✓ Clean	`c1cc(ccc1CN)Br`
WO4	1Z7M	Q02147	247.8 Da LogP -2.62 TPSA 80.3	✓ Ro5	✓ Clean	`[O-][W](=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
HSS	P12081	6.89	483.5 Da LogP -3.30 TPSA 246.5	2 viol.	✓ Clean	`c1c([nH]cn1)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]2[C@…`

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
ZINC2528975	0.842	215.3 Da LogP 3.66 TPSA 26.0	✓ Ro5	✓ Clean	`CSc1ccc(-c2ccc(N)cc2)cc1`
ZINC4204203	0.842	218.7 Da LogP 3.50 TPSA 20.2	✓ Ro5	✓ Clean	`OCc1ccc(-c2ccc(Cl)cc2)cc1`
ZINC5763414	0.842	262.1 Da LogP 3.57 TPSA 26.0	✓ Ro5	✓ Clean	`NCc1ccc(-c2ccc(Br)cc2)cc1`
ZINC45870402	0.789	214.3 Da LogP 2.97 TPSA 42.0	✓ Ro5	✓ Clean	`CCCC(=O)Nc1cnc2ccccc2c1`
ZINC12754784	0.784	305.3 Da LogP 3.45 TPSA 71.1	✓ Ro5	✓ Clean	`CC(=O)Nc1ccc(C(=O)Nc2cnc3ccccc3c2)cc1`
ZINC12790818	0.781	314.3 Da LogP 4.43 TPSA 66.9	✓ Ro5	✓ Clean	`O=C(Nc1cnc2ccccc2c1)Nc1cnc2ccccc2c1`
ZINC25155856	0.750	228.3 Da LogP 3.36 TPSA 42.0	✓ Ro5	✓ Clean	`CCCCC(=O)Nc1cnc2ccccc2c1`
ZINC12754779	0.744	319.4 Da LogP 3.37 TPSA 71.1	✓ Ro5	✓ Clean	`CC(=O)Nc1ccc(CC(=O)Nc2cnc3ccccc3c2)cc1`
ZINC23353076	0.744	228.3 Da LogP 3.22 TPSA 42.0	✓ Ro5	✓ Clean	`CC(C)CC(=O)Nc1cnc2ccccc2c1`
ZINC37020264	0.737	201.2 Da LogP 1.13 TPSA 68.0	✓ Ro5	✓ Clean	`NCC(=O)Nc1cnc2ccccc2c1`
ZINC20435359	0.727	234.7 Da LogP 3.62 TPSA 29.5	✓ Ro5	✓ Clean	`OCc1ccc(Oc2ccc(Cl)cc2)cc1`
ZINC20470234	0.727	278.1 Da LogP 3.70 TPSA 35.2	✓ Ro5	✓ Clean	`NCc1ccc(Oc2ccc(Br)cc2)cc1`
ZINC479347	0.727	250.8 Da LogP 3.98 TPSA 20.2	✓ Ro5	✓ Clean	`OCc1ccc(Sc2ccc(Cl)cc2)cc1`
ZINC32906940	0.725	216.2 Da LogP 1.82 TPSA 51.2	✓ Ro5	✓ Clean	`COCC(=O)Nc1cnc2ccccc2c1`
ZINC206786	0.722	215.3 Da LogP 2.33 TPSA 45.2	✓ Ro5	✓ Clean	`CN(C)C(=O)Nc1cnc2ccccc2c1`
ZINC781947	0.722	214.3 Da LogP 2.83 TPSA 42.0	✓ Ro5	✓ Clean	`CC(C)C(=O)Nc1cnc2ccccc2c1`
ZINC49581950	0.720	202.1 Da LogP 1.38 TPSA 33.1	✓ Ro5	✓ Clean	`OCCc1cccc(Br)n1`
ZINC13208214	0.714	263.3 Da LogP 3.88 TPSA 54.0	✓ Ro5	✓ Clean	`O=C(Nc1ccccc1)Nc1cnc2ccccc2c1`
ZINC24929580	0.707	242.3 Da LogP 3.61 TPSA 42.0	✓ Ro5	✓ Clean	`CC(C)CCC(=O)Nc1cnc2ccccc2c1`
ZINC13283022	0.703	262.3 Da LogP 3.86 TPSA 42.0	✓ Ro5	✓ Clean	`CC(=O)Nc1ccc(-c2cnc3ccccc3c2)cc1`
ZINC2325815868	0.700	218.2 Da LogP 2.72 TPSA 42.0	✓ Ro5	✓ Clean	`CCC(=O)Nc1cnc2ccc(F)cc2c1`
ZINC299397	0.700	243.3 Da LogP 3.11 TPSA 45.2	✓ Ro5	✓ Clean	`CCN(CC)C(=O)Nc1cnc2ccccc2c1`
ZINC417944	0.700	244.3 Da LogP 2.04 TPSA 79.3	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)Nc1cnc2ccccc2c1`
ZINC13208234	0.694	240.2 Da LogP 2.74 TPSA 42.0	✓ Ro5	✓ Clean	`O=C(Nc1cnc2ccccc2c1)C(F)(F)F`
ZINC12645336	0.690	276.3 Da LogP 3.72 TPSA 42.0	✓ Ro5	✓ Clean	`Cc1ccc(CC(=O)Nc2cnc3ccccc3c2)cc1`
ZINC21137511	0.690	331.4 Da LogP 3.85 TPSA 71.1	✓ Ro5	✓ Clean	`CC(=O)Nc1ccc(/C=C/C(=O)Nc2cnc3ccccc3c2)cc1`
ZINC30931304	0.690	246.3 Da LogP 2.93 TPSA 42.0	✓ Ro5	✓ Clean	`CSCCC(=O)Nc1cnc2ccccc2c1`
ZINC37867231	0.684	277.3 Da LogP 4.19 TPSA 54.0	✓ Ro5	✓ Clean	`Cc1ccc(NC(=O)Nc2cnc3ccccc3c2)cc1`
ZINC40921709	0.684	229.3 Da LogP 1.91 TPSA 68.0	✓ Ro5	✓ Clean	`CC(C)(N)C(=O)Nc1cnc2ccccc2c1`
ZINC9875203	0.684	291.4 Da LogP 4.50 TPSA 54.0	✓ Ro5	✓ Clean	`Cc1cc(C)cc(NC(=O)Nc2cnc3ccccc3c2)c1`
ZINC1668658	0.683	216.2 Da LogP 2.80 TPSA 51.2	✓ Ro5	✓ Clean	`CCOC(=O)Nc1cnc2ccccc2c1`
ZINC21136962	0.683	285.3 Da LogP 2.33 TPSA 71.1	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](C(=O)Nc1cnc2ccccc2c1)C(C)C`
ZINC21136965	0.683	285.3 Da LogP 2.33 TPSA 71.1	✓ Ro5	✓ Clean	`CC(=O)N[C@H](C(=O)Nc1cnc2ccccc2c1)C(C)C`
ZINC25157050	0.682	272.3 Da LogP 2.52 TPSA 68.3	✓ Ro5	✓ Clean	`CCOC(=O)CCC(=O)Nc1cnc2ccccc2c1`
ZINC2574307	0.680	200.1 Da LogP 1.95 TPSA 26.0	✓ Ro5	✓ Clean	`NCCc1cccc(Br)c1`
ZINC24754608	0.674	260.4 Da LogP 3.31 TPSA 42.0	✓ Ro5	✓ Clean	`CC(C)SCC(=O)Nc1cnc2ccccc2c1`
ZINC100818	0.667	280.3 Da LogP 3.56 TPSA 42.0	✓ Ro5	✓ Clean	`O=C(Cc1ccc(F)cc1)Nc1cnc2ccccc2c1`
ZINC12754822	0.667	276.3 Da LogP 3.81 TPSA 42.0	✓ Ro5	✓ Clean	`O=C(CCc1ccccc1)Nc1cnc2ccccc2c1`
ZINC23075087	0.667	312.4 Da LogP 4.57 TPSA 42.0	✓ Ro5	✓ Clean	`O=C(Cc1ccc2ccccc2c1)Nc1cnc2ccccc2c1`
ZINC24754622	0.667	274.4 Da LogP 3.71 TPSA 42.0	✓ Ro5	✓ Clean	`CCCCSCC(=O)Nc1cnc2ccccc2c1`
ZINC27103595	0.667	201.2 Da LogP 2.88 TPSA 31.4	✓ Ro5	✓ Clean	`COc1cccc(Oc2cccnc2)c1`
ZINC460059	0.667	277.3 Da LogP 3.90 TPSA 45.2	✓ Ro5	✓ Clean	`CN(C(=O)Nc1cnc2ccccc2c1)c1ccccc1`
ZINC616194	0.667	262.3 Da LogP 3.80 TPSA 42.0	✓ Ro5	✓ Clean	`Cc1ccc(C(=O)Nc2cnc3ccccc3c2)cc1`
ZINC71773889	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@H](O)C(=O)O)C[C@H](O)C(=O)O`
ZINC71773890	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@H](O)C(=O)O)C[C@@H](O)C(=O)O`
ZINC71773891	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@@H](O)C(=O)O)C[C@@H](O)C(=O)O`
ZINC23353266	0.659	290.4 Da LogP 4.37 TPSA 42.0	✓ Ro5	✓ Clean	`C[C@@H](CC(=O)Nc1cnc2ccccc2c1)c1ccccc1`
ZINC23353269	0.659	290.4 Da LogP 4.37 TPSA 42.0	✓ Ro5	✓ Clean	`C[C@H](CC(=O)Nc1cnc2ccccc2c1)c1ccccc1`
ZINC58003969	0.659	255.3 Da LogP 2.27 TPSA 45.2	✓ Ro5	✓ Clean	`CN(CC(=O)Nc1cnc2ccccc2c1)C1CC1`
ZINC53024	0.658	281.3 Da LogP 4.02 TPSA 54.0	✓ Ro5	✓ Clean	`O=C(Nc1ccc(F)cc1)Nc1cnc2ccccc2c1`

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.