Protein profile

KP13_05165

Pyridoxamine kinase

Genome: KpKP13

Gene: AHE44284.1 pdxY Structure source: AlphaFold + ColabFold UniProt A0A0H3GUH0

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Amino acids 286

Annotations 6

Features 16

PDB binders 13

Druggability 0.7

Overview

Basic information about this protein and its source genome.

Accession: KP13_05165
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44284.1 pdxY
Status: annotated
Amino acids: 286
Structure source: AlphaFold + ColabFold

2.7.1.35

GO:0009443 Any process that generates pyridoxal 5'-phosphate, the active form of vitamin B6, from derivatives of it without de novo synthesis. GO:0008478 Catalysis of the reaction: ATP + pyridoxal = ADP + pyridoxal 5'-phosphate. 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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 54.762
Human E-value: 8.2e-09
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 50.694
DEG E-value: 6.52e-99
Localization: Cytoplasmic
ColabFold pLDDT: 97.48

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 0.7

Structure A0A0H3GUH0

Pocket Pocket 1

P2Rank 0.963

Structure A0A0H3GUH0

Pocket Pocket 1

ColabFold model

FPocket 0.687 · Pocket 3

P2Rank 0.963 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 121 / 4744 genomes with a hit

Normalized 0.026

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:0009443 Any process that generates pyridoxal 5'-phosphate, the active form of vitamin B6, from derivatives of it without de novo synthesis.
GO:0008478 Catalysis of the reaction: ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
2	279	PANTHER	PTHR10534	PYRIDOXAL KINASE
2	279	InterPro	IPR004625	Pyridoxine kinase
1	285	NCBIfam	TIGR00687	pyridoxal kinase
1	285	InterPro	IPR004625	Pyridoxine kinase
253	273	Coils	Coil	Coil
1	286	Gene3D	G3DSA:3.40.1190.20	-
1	286	InterPro	IPR029056	Ribokinase-like
1	278	SUPERFAMILY	SSF53613	Ribokinase-like
1	278	InterPro	IPR029056	Ribokinase-like
3	257	CDD	cd01173	pyridoxal_pyridoxamine_kinase
3	257	InterPro	IPR004625	Pyridoxine kinase
1	286	FunFam	G3DSA:3.40.1190.20:FF:000008	Pyridoxal kinase PdxY
1	286	Hamap	MF_01639	Pyridoxal kinase PdxY [pdxY].
1	286	InterPro	IPR023685	Pyridoxal kinase PdxY
74	257	Pfam	PF08543	Phosphomethylpyrimidine kinase
74	257	InterPro	IPR013749	Pyridoxamine kinase/Phosphomethylpyrimidine kinase

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_A0A0H3GUH0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05165	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				0.7

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				30.9	0.936
2				1.68	0.029

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				0.687
1				0.642

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				31.92	0.941
2				1.61	0.026

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.