Protein profile

PA5516

pyridoxamine kinase

Genome: NC_002516.2

Gene: PA5516 pdxY Structure source: Experimental + AlphaFold UniProt Q9HT57

Export view

Amino acids 288

Annotations 6

Features 20

PDB binders 13

Druggability 0.824

Overview

Basic information about this protein and its source genome.

Accession: PA5516
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA5516 pdxY
Status: annotated
Amino acids: 288
Structure source: Experimental + AlphaFold

2.7.1.35

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0000287 Binding to a magnesium (Mg) ion. GO:0008478 Catalysis of the reaction: ATP + pyridoxal = ADP + pyridoxal 5'-phosphate. GO:0009443 Any process that generates pyridoxal 5'-phosphate, the active form of vitamin B6, from derivatives of it without de novo synthesis.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 50.0
Human E-value: 3.11e-09
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 0.824

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

2.7.1.35

Gene Ontology (GO)

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0000287 Binding to a magnesium (Mg) ion.
GO:0008478 Catalysis of the reaction: ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.
GO:0009443 Any process that generates pyridoxal 5'-phosphate, the active form of vitamin B6, from derivatives of it without de novo synthesis.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
1	22	Phobius	SIGNAL_PEPTIDE	Signal peptide region
4	280	PANTHER	PTHR10534	PYRIDOXAL KINASE
4	280	InterPro	IPR004625	Pyridoxine kinase
1	288	Gene3D	G3DSA:3.40.1190.20	-
1	288	InterPro	IPR029056	Ribokinase-like
6	287	NCBIfam	TIGR00687	pyridoxal kinase
6	287	InterPro	IPR004625	Pyridoxine kinase
4	288	Hamap	MF_01639	Pyridoxal kinase PdxY [pdxY].
4	288	InterPro	IPR023685	Pyridoxal kinase PdxY
77	262	Pfam	PF08543	Phosphomethylpyrimidine kinase
77	262	InterPro	IPR013749	Pyridoxamine kinase/Phosphomethylpyrimidine kinase
1	6	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
3	288	FunFam	G3DSA:3.40.1190.20:FF:000008	Pyridoxal kinase PdxY
18	22	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
4	281	SUPERFAMILY	SSF53613	Ribokinase-like
4	281	InterPro	IPR029056	Ribokinase-like
7	261	CDD	cd01173	pyridoxal_pyridoxamine_kinase
7	261	InterPro	IPR004625	Pyridoxine kinase
7	17	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
23	288	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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...

Legend High Medium Low

Structural evidence

1 + 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 5B6A	X-ray	2.00 Å	A	100.0% 1-288	PDBe RCSB PDBj File	Viewing
AlphaFold PA5516	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
1				0.824
3				0.348

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				31.4	0.939

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				0.826

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.

68 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
ACP	1RFT	P82197	505.2 Da LogP -1.52 TPSA 269.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
AGS	6YK0	Q8K183	523.2 Da LogP -1.51 TPSA 262.1	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
ANP	2AJP	O00764	506.2 Da LogP -2.06 TPSA 281.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
D95	6YK1	Q8K183	384.4 Da LogP 2.60 TPSA 100.5	✓ Ro5	✓ Clean	`C[C@@H]1CC[C@H]2[C@H]([C@@H](O[C@H]3[C@@]24[C@H…`
GT0	4EN4	O00764	183.2 Da LogP 0.73 TPSA 62.6	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)CO)COC)O`
GT1	4EN4	O00764	263.2 Da LogP 0.85 TPSA 109.1	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)COC)O`
NHE	5TRW	Q141E8	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCS(=O)(=O)O`
PXL	1TD2	P77150	167.2 Da LogP 0.40 TPSA 70.4	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)CO)C=O)O`
PXM	1RFT	P82197	168.2 Da LogP 0.05 TPSA 79.4	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)CO)CN)O`
R6C	1YHJ	P82197	355.4 Da LogP 3.17 TPSA 85.1	✓ Ro5	✓ Clean	`CC[C@H](CO)Nc1nc2c(c(n1)OCc3ccccc3)ncn2C(C)C`
RMC	1YGJ	P82197	368.5 Da LogP 3.23 TPSA 79.1	✓ Ro5	✓ Clean	`CC[C@H](CO)Nc1nc2c(c(n1)[N@@](C)Cc3ccccc3)ncn2C…`
RRC	1YGK	P82197	354.5 Da LogP 3.20 TPSA 87.9	✓ Ro5	✓ Clean	`CC[C@H](CO)Nc1nc(c2c(n1)n(cn2)C(C)C)NCc3ccccc3`
TEP	4EOH	O00764	180.2 Da LogP -1.04 TPSA 72.7	✓ Ro5	✓ Clean	`CN1c2c([nH]cn2)C(=O)N(C1=O)C`

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
DXH	O00764	8.29	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cnn(c3nc(n2)c4cccnc4)C)C(=O)Nc5c…`
CHEMBL1233528	O00764	6.54	618.8 Da LogP 4.27 TPSA 106.2	1 viol.	✓ Clean	`CC[C@@H]1C(=O)N(C)c2cnc(Nc3ccc(C(=O)N[C@H]4CC[C…`
R78	O00764	6.41	521.7 Da LogP 3.56 TPSA 102.9	1 viol.	✓ Clean	`CC[C@@H]1C(=O)N(c2cnc(nc2N1C3CCCC3)Nc4ccc(cc4OC…`
71T	O00764	—	454.6 Da LogP 3.67 TPSA 66.9	✓ Ro5	Alert	`COc1ccc(cc1)N2CCN(CC2)C(=O)c3cc4c(s3)-c5ccccc5S…`
CHEMBL3944678	O00764	—	923.2 Da LogP 3.73 TPSA 195.6	2 viol.	Alert	`O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]21)NCCOCCO…`

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
ZINC111941930	1.000	368.5 Da LogP 3.23 TPSA 79.1	✓ Ro5	✓ Clean	`CC[C@@H](CO)Nc1nc(N(C)Cc2ccccc2)c2ncn(C(C)C)c2n1`
ZINC12504508	1.000	368.5 Da LogP 3.23 TPSA 79.1	✓ Ro5	✓ Clean	`CC[C@H](CO)Nc1nc(N(C)Cc2ccccc2)c2ncn(C(C)C)c2n1`
ZINC1649340	1.000	354.5 Da LogP 3.20 TPSA 87.9	✓ Ro5	✓ Clean	`CC[C@H](CO)Nc1nc(NCc2ccccc2)c2ncn(C(C)C)c2n1`
ZINC1710230	1.000	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC602192	1.000	354.5 Da LogP 3.20 TPSA 87.9	✓ Ro5	✓ Clean	`CC[C@@H](CO)Nc1nc(NCc2ccccc2)c2ncn(C(C)C)c2n1`
ZINC64608163	1.000	384.4 Da LogP 2.60 TPSA 100.5	✓ Ro5	✓ Clean	`C[C@@H]1[C@H](OC(=O)CCC(=O)O)O[C@H]2O[C@@]3(C)C…`
ZINC9407519	1.000	454.6 Da LogP 3.67 TPSA 66.9	✓ Ro5	Alert	`COc1ccc(N2CCN(C(=O)c3cc4c(s3)-c3ccccc3S(=O)(=O)…`
ZINC105469665	0.873	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)CP(=O…`
ZINC13527614	0.873	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)CP(=O)…`
ZINC219330894	0.873	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873852	0.873	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873853	0.873	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)CP(=O…`
ZINC3873854	0.873	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873855	0.873	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)CP(=O…`
ZINC35997756	0.843	425.5 Da LogP 3.43 TPSA 107.9	✓ Ro5	✓ Clean	`CC[C@@H]1C(=O)N(C)c2cnc(Nc3ccc(C(=O)O)cc3OC)nc2…`
ZINC12360002	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC31977053	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC12504456	0.804	370.5 Da LogP 2.91 TPSA 108.1	✓ Ro5	Alert	`CC[C@H](CO)Nc1nc(NCc2ccccc2O)c2ncn(C(C)C)c2n1`
ZINC13819459	0.804	370.5 Da LogP 2.91 TPSA 108.1	✓ Ro5	Alert	`CC[C@@H](CO)Nc1nc(NCc2ccccc2O)c2ncn(C(C)C)c2n1`
ZINC16052806	0.800	431.5 Da LogP 4.26 TPSA 100.8	✓ Ro5	✓ Clean	`CC[C@@H](CO)Nc1nc(NCc2ccc(-c3ccccn3)cc2)c2ncn(C…`
ZINC16052807	0.800	431.5 Da LogP 4.26 TPSA 100.8	✓ Ro5	✓ Clean	`CC[C@H](CO)Nc1nc(NCc2ccc(-c3ccccn3)cc2)c2ncn(C(…`
ZINC2004372	0.786	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153	0.786	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
ZINC13518964	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.768	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	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.768	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	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC40846490	0.762	431.5 Da LogP 4.26 TPSA 100.8	✓ Ro5	✓ Clean	`CC[C@H](CO)Nc1nc(NCc2cccc(-c3ccccn3)c2)c2ncn(C(…`
ZINC106362085	0.758	455.5 Da LogP 2.11 TPSA 129.6	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)CCC(=O)O[C@@H]1O[C@@H]2O[C@]3(C)C…`
ZINC200028557	0.754	354.5 Da LogP 3.03 TPSA 87.9	✓ Ro5	✓ Clean	`CCCn1cnc2c(NCc3ccccc3)nc(N[C@@H](CC)CO)nc21`
ZINC4096224	0.754	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC95558175	0.754	354.5 Da LogP 3.03 TPSA 87.9	✓ Ro5	✓ Clean	`CCCn1cnc2c(NCc3ccccc3)nc(N[C@H](CC)CO)nc21`

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.