Protein profile

PA4279

pantothenate kinase

Genome: NC_002516.2

Gene: coaA coaX PA4279 Structure source: Experimental + AlphaFold UniProt Q9HWC1

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Amino acids 248

Annotations 7

Features 14

PDB binders 2

Druggability 0.402

Overview

Basic information about this protein and its source genome.

Accession: PA4279
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: coaA coaX PA4279
Status: annotated
Amino acids: 248
Structure source: Experimental + AlphaFold

2.7.1.33

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0046872 Binding to a metal ion. GO:0004594 Catalysis of the reaction: ATP + pantothenate = ADP + D-4'-phosphopantothenate. GO:0015937 The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester. GO:0046677 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
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 0.402

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

2.7.1.33

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0046872 Binding to a metal ion.
GO:0004594 Catalysis of the reaction: ATP + pantothenate = ADP + D-4'-phosphopantothenate.
GO:0015937 The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
GO:0046677 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
117	234	Gene3D	G3DSA:3.30.420.40	-
1	245	PANTHER	PTHR34265	TYPE III PANTOTHENATE KINASE
1	245	InterPro	IPR004619	Type III pantothenate kinase
3	243	NCBIfam	TIGR00671	type III pantothenate kinase
3	243	InterPro	IPR004619	Type III pantothenate kinase
1	248	Hamap	MF_01274	Type III pantothenate kinase [coaX].
1	248	InterPro	IPR004619	Type III pantothenate kinase
116	245	SUPERFAMILY	SSF53067	Actin-like ATPase domain
116	245	InterPro	IPR043129	ATPase, nucleotide binding domain
5	241	Gene3D	G3DSA:3.30.420.40	-
2	200	Pfam	PF03309	Type III pantothenate kinase
2	200	InterPro	IPR004619	Type III pantothenate kinase
1	113	SUPERFAMILY	SSF53067	Actin-like ATPase domain
1	113	InterPro	IPR043129	ATPase, nucleotide binding domain

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

2 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 2F9W	X-ray	1.90 Å	A,B	100.0% 1-248	PDBe RCSB PDBj File	Viewing
PDB 2F9T	X-ray	2.20 Å	A,B	100.0% 1-248	PDBe RCSB PDBj File	Loaded
AlphaFold PA4279	AlphaFold	—	—	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
3				0.402
2				0.275

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				20.18	0.851
2				0.81	0.003

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
5				0.937
3				0.797

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.

46 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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
PAU	2F9W 1.90 Å Open crystal	219.2 Da LogP -1.04 TPSA 106.9	✓ Ro5	✓ Clean	`CC(C)(CO)[C@H](C(=O)NCCC(=O)O)O`

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
2PN	5B8H	B4E9P3	177.0 Da LogP -1.24 TPSA 127.1	✓ Ro5	✓ Clean	`N(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).

Ligand	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL4279314	—	302.3 Da LogP -0.94 TPSA 132.8	✓ Ro5	✓ Clean	`CC(=O)CC(=O)NCC(C)(C)[C@@H](O)C(=O)NCCC(=O)O`
CHEMBL4290263	—	232.3 Da LogP -0.82 TPSA 98.7	✓ Ro5	✓ Clean	`CNCC(C)(C)[C@@H](O)C(=O)NCCC(=O)O`
CHEMBL4292981	—	233.3 Da LogP -0.39 TPSA 95.9	✓ Ro5	✓ Clean	`COCC(C)(C)[C@@H](O)C(=O)NCCC(=O)O`

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
ZINC5356858	1.000	219.2 Da LogP -1.04 TPSA 106.9	✓ Ro5	✓ Clean	`CC(C)(CO)[C@H](O)C(=O)NCCC(=O)O`
ZINC5356910	1.000	219.2 Da LogP -1.04 TPSA 106.9	✓ Ro5	✓ Clean	`CC(C)(CO)[C@@H](O)C(=O)NCCC(=O)O`
ZINC2017228	0.800	233.3 Da LogP -0.65 TPSA 106.9	✓ Ro5	✓ Clean	`CC(C)(CO)[C@@H](O)C(=O)NCCCC(=O)O`
ZINC2018156	0.800	233.3 Da LogP -0.65 TPSA 106.9	✓ Ro5	✓ Clean	`CC(C)(CO)[C@H](O)C(=O)NCCCC(=O)O`
ZINC4026897	0.750	261.3 Da LogP 0.13 TPSA 106.9	✓ Ro5	✓ Clean	`CC(C)(CO)[C@H](O)C(=O)NCCCCCC(=O)O`
ZINC4026898	0.750	261.3 Da LogP 0.13 TPSA 106.9	✓ Ro5	✓ Clean	`CC(C)(CO)[C@@H](O)C(=O)NCCCCCC(=O)O`
ZINC5356918	0.688	233.3 Da LogP -0.95 TPSA 95.9	✓ Ro5	✓ Clean	`COC(=O)CCNC(=O)[C@H](O)C(C)(C)CO`
ZINC1530303	0.645	205.3 Da LogP -1.14 TPSA 89.8	✓ Ro5	✓ Clean	`CC(C)(CO)[C@@H](O)C(=O)NCCCO`
ZINC1567243	0.645	205.3 Da LogP -1.14 TPSA 89.8	✓ Ro5	✓ Clean	`CC(C)(CO)[C@H](O)C(=O)NCCCO`
ZINC14637066	0.629	247.3 Da LogP -0.56 TPSA 95.9	✓ Ro5	✓ Clean	`CCOC(=O)CCNC(=O)[C@@H](O)C(C)(C)CO`
ZINC14637068	0.629	247.3 Da LogP -0.56 TPSA 95.9	✓ Ro5	✓ Clean	`CCOC(=O)CCNC(=O)[C@H](O)C(C)(C)CO`
ZINC3869683	0.629	278.4 Da LogP -1.08 TPSA 98.7	✓ Ro5	✓ Clean	`CC(C)(CO)[C@H](O)C(=O)NCCC(=O)NCCS`
ZINC3869684	0.629	278.4 Da LogP -1.08 TPSA 98.7	✓ Ro5	✓ Clean	`CC(C)(CO)[C@@H](O)C(=O)NCCC(=O)NCCS`
ZINC85223882	0.629	261.3 Da LogP -2.05 TPSA 124.7	✓ Ro5	✓ Clean	`CC(C)(CO)[C@@H](O)C(=O)NCCC(=O)NCCN`
ZINC1700914	0.622	279.3 Da LogP 0.75 TPSA 86.6	✓ Ro5	✓ Clean	`CC(C)(CO)[C@H](O)C(=O)NCCC(=O)c1ccccc1`
ZINC5434605	0.622	279.3 Da LogP 0.75 TPSA 86.6	✓ Ro5	✓ Clean	`CC(C)(CO)[C@@H](O)C(=O)NCCC(=O)c1ccccc1`
ZINC1882721	0.606	277.3 Da LogP -1.05 TPSA 127.1	✓ Ro5	✓ Clean	`CC(C)(CNC(=O)[C@H](O)C(C)(C)CO)[C@H](O)C(=O)O`
ZINC1882723	0.606	277.3 Da LogP -1.05 TPSA 127.1	✓ Ro5	✓ Clean	`CC(C)(CNC(=O)[C@@H](O)C(C)(C)CO)[C@H](O)C(=O)O`
ZINC1882725	0.606	277.3 Da LogP -1.05 TPSA 127.1	✓ Ro5	✓ Clean	`CC(C)(CNC(=O)[C@H](O)C(C)(C)CO)[C@@H](O)C(=O)O`
ZINC1882727	0.606	277.3 Da LogP -1.05 TPSA 127.1	✓ Ro5	✓ Clean	`CC(C)(CO)[C@H](O)C(=O)NCC(C)(C)[C@@H](O)C(=O)O`
ZINC4096306	0.590	322.4 Da LogP -1.63 TPSA 136.0	1 viol.	✓ Clean	`CC(C)(CO)[C@@H](O)C(=O)NCCC(=O)N[C@@H](CS)C(=O)O`
ZINC72318677	0.590	293.4 Da LogP 0.68 TPSA 86.6	✓ Ro5	✓ Clean	`CC(C)(CO)[C@@H](O)C(=O)NCCC(=O)Cc1ccccc1`
ZINC1666581	0.588	255.3 Da LogP -1.63 TPSA 123.9	✓ Ro5	✓ Clean	`CC(C)(CO)[C@H](O)C(=O)NCCS(=O)(=O)O`
ZINC1711129	0.588	255.3 Da LogP -1.63 TPSA 123.9	✓ Ro5	✓ Clean	`CC(C)(CO)[C@@H](O)C(=O)NCCS(=O)(=O)O`
ZINC2026810	0.588	200.2 Da LogP -0.60 TPSA 93.3	✓ Ro5	✓ Clean	`CC(C)(CO)[C@H](O)C(=O)NCCC#N`
ZINC2026813	0.588	200.2 Da LogP -0.60 TPSA 93.3	✓ Ro5	✓ Clean	`CC(C)(CO)[C@@H](O)C(=O)NCCC#N`
ZINC2040273	0.576	219.2 Da LogP -0.90 TPSA 106.9	✓ Ro5	✓ Clean	`CC(C)(O)C[C@H](O)C(=O)NCCC(=O)O`
ZINC2040274	0.576	219.2 Da LogP -0.90 TPSA 106.9	✓ Ro5	✓ Clean	`CC(C)(O)C[C@@H](O)C(=O)NCCC(=O)O`
ZINC3158398	0.556	269.3 Da LogP -1.24 TPSA 123.9	✓ Ro5	✓ Clean	`CC(C)(CO)[C@H](O)C(=O)NCCCS(=O)(=O)O`
ZINC3158399	0.556	269.3 Da LogP -1.24 TPSA 123.9	✓ Ro5	✓ Clean	`CC(C)(CO)[C@@H](O)C(=O)NCCCS(=O)(=O)O`
ZINC2568351	0.541	233.3 Da LogP -0.09 TPSA 78.8	✓ Ro5	✓ Clean	`CCOCCCNC(=O)[C@@H](O)C(C)(C)CO`
ZINC2573526	0.541	233.3 Da LogP -0.09 TPSA 78.8	✓ Ro5	✓ Clean	`CCOCCCNC(=O)[C@H](O)C(C)(C)CO`
ZINC257358027	0.528	311.3 Da LogP -4.08 TPSA 170.7	1 viol.	✓ Clean	`CC(C)(CO)[C@H](O)C(=O)NC[C@H](O)[C@H](O)[C@@H](…`
ZINC257358028	0.528	311.3 Da LogP -4.08 TPSA 170.7	1 viol.	✓ Clean	`CC(C)(CO)[C@H](O)C(=O)NC[C@H](O)[C@H](O)[C@@H](…`
ZINC257358029	0.528	311.3 Da LogP -4.08 TPSA 170.7	1 viol.	✓ Clean	`CC(C)(CO)[C@H](O)C(=O)NC[C@H](O)[C@H](O)[C@H](O…`
ZINC71769816	0.528	311.3 Da LogP -4.08 TPSA 170.7	1 viol.	✓ Clean	`CC(C)(CO)[C@H](O)C(=O)NC[C@H](O)[C@H](O)[C@H](O…`
ZINC101175288	0.516	261.2 Da LogP -2.50 TPSA 158.8	✓ Ro5	✓ Clean	`NC(C(=O)NCCC(=O)O)C(=O)NCCC(=O)O`
ZINC4655869	0.513	281.3 Da LogP 0.38 TPSA 106.9	✓ Ro5	✓ Clean	`CC(C)(CO)[C@H](O)C(=O)NCc1ccc(C(=O)O)cc1`
ZINC4728762	0.513	281.3 Da LogP 0.38 TPSA 106.9	✓ Ro5	✓ Clean	`CC(C)(CO)[C@@H](O)C(=O)NCc1ccc(C(=O)O)cc1`
ZINC1676593	0.512	362.3 Da LogP 2.37 TPSA 86.6	✓ Ro5	✓ Clean	`Cc1cc(Cl)c(Cl)cc1C(=O)CCNC(=O)[C@H](O)C(C)(C)CO`
ZINC2045472	0.512	362.3 Da LogP 2.37 TPSA 86.6	✓ Ro5	✓ Clean	`Cc1cc(Cl)c(Cl)cc1C(=O)CCNC(=O)[C@@H](O)C(C)(C)CO`

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.