Protein profile

KP13_03430

Choline dehydrogenase

Genome: KpKP13

Gene: AHE45805.1 betA Structure source: AlphaFold + ColabFold UniProt A0A0H3GL29

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Amino acids 554

Annotations 8

Features 22

PDB binders 7

Druggability 0.877

Overview

Basic information about this protein and its source genome.

Accession: KP13_03430
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45805.1 betA
Status: annotated
Amino acids: 554
Structure source: AlphaFold + ColabFold

1.1.99.1 1.2.1.8

GO:0019285 The chemical reactions and pathways resulting in the formation of betaine (N-trimethylglycine) from the oxidation of choline. GO:0016614 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor. GO:0008812 Catalysis of the reaction: A + choline = AH(2) + betaine aldehyde. GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0008802 Catalysis of the reaction: betaine aldehyde + NAD+ + H2O = betaine + NADH + H+.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 47.849
Human E-value: 4.62e-171
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 96.02

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 0.877

Structure A0A0H3GL29

Pocket Pocket 1

P2Rank 0.983

Structure A0A0H3GL29

Pocket Pocket 1

ColabFold model

FPocket 0.992 · Pocket 1

P2Rank 0.991 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 91 / 4744 genomes with a hit

Normalized 0.019

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 6 GO

Enzyme Commission (EC)

Gene Ontology (GO)

GO:0019285 The chemical reactions and pathways resulting in the formation of betaine (N-trimethylglycine) from the oxidation of choline.
GO:0016614 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
GO:0008812 Catalysis of the reaction: A + choline = AH(2) + betaine aldehyde.
GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0008802 Catalysis of the reaction: betaine aldehyde + NAD+ + H2O = betaine + NADH + H+.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records

Show feature table

Start	End	DB	Term	Name
82	105	ProSitePatterns	PS00623	GMC oxidoreductases signature 1.
82	105	InterPro	IPR000172	Glucose-methanol-choline oxidoreductase, N-terminal
259	273	ProSitePatterns	PS00624	GMC oxidoreductases signature 2.
259	273	InterPro	IPR000172	Glucose-methanol-choline oxidoreductase, N-terminal
1	535	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
1	535	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
1	538	PIRSF	PIRSF000137	Alcohol_oxidase
1	538	InterPro	IPR012132	Glucose-methanol-choline oxidoreductase
3	539	PANTHER	PTHR11552	GLUCOSE-METHANOL-CHOLINE GMC OXIDOREDUCTASE
3	539	InterPro	IPR012132	Glucose-methanol-choline oxidoreductase
1	554	Hamap	MF_00750	Oxygen-dependent choline dehydrogenase [betA].
1	554	InterPro	IPR011533	Oxygen-dependent choline dehydrogenase
295	477	SUPERFAMILY	SSF54373	FAD-linked reductases, C-terminal domain
3	300	Pfam	PF00732	GMC oxidoreductase
3	300	InterPro	IPR000172	Glucose-methanol-choline oxidoreductase, N-terminal
393	527	Pfam	PF05199	GMC oxidoreductase
393	527	InterPro	IPR007867	Glucose-methanol-choline oxidoreductase, C-terminal
4	537	NCBIfam	TIGR01810	choline dehydrogenase
4	537	InterPro	IPR011533	Oxygen-dependent choline dehydrogenase
43	472	Gene3D	G3DSA:3.30.560.10	Glucose Oxidase, domain 3
4	525	Gene3D	G3DSA:3.50.50.60	-
4	525	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily

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_A0A0H3GL29	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03430	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				0.877
2				0.777

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	Score	Probability
1	38.78	0.96
2	13.86	0.701
3	1.79	0.033

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				0.992
17				0.868

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	Score	Probability
1	47.69	0.976
2	8.6	0.459
3	1.84	0.035
4	1.75	0.032
5	1.41	0.018

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.

57 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
ANN	5OC1	O94219	152.1 Da LogP 1.39 TPSA 46.5	✓ Ro5	✓ Clean	`COc1ccc(cc1)C(=O)O`
BET	4MJW	Q7X2H8	118.2 Da LogP -0.22 TPSA 37.3	✓ Ro5	✓ Clean	`C[N+](C)(C)CC(=O)O`
FAO	2JBV	Q7X2H8	789.6 Da LogP -2.56 TPSA 355.8	3 viol.	✓ Clean	`Cc1cc2c(cc1C)[N@@]([C@@H]3[C@H](N2)C(=O)NC(=O)N…`
FDA	4YNT	B8MX95	787.6 Da LogP -1.75 TPSA 363.3	3 viol.	✓ Clean	`Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C…`
PLM	5NCC	A0A248QE08	256.4 Da LogP 5.55 TPSA 37.3	1 viol.	✓ Clean	`CCCCCCCCCCCCCCCC(=O)O`
PXM	4HA6	Q5NT46	168.2 Da LogP 0.05 TPSA 79.4	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)CO)CN)O`
STE	6ZH7	A0A248QE08	284.5 Da LogP 6.33 TPSA 37.3	1 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCC(=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).

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
ZINC1529498	1.000	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1530417	1.000	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
ZINC1628119	1.000	214.3 Da LogP 4.38 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)O`
ZINC11802360	0.870	244.2 Da LogP 3.19 TPSA 55.8	✓ Ro5	✓ Clean	`COc1ccc(Oc2ccc(C(=O)O)cc2)cc1`
ZINC1514433	0.870	228.2 Da LogP 3.06 TPSA 46.5	✓ Ro5	✓ Clean	`COc1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC138457918	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCC(=O)O`
ZINC138458029	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCC(=O)O`
ZINC144395054	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCC(=O)O`
ZINC14619628	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCCCC(=O)O`
ZINC196749828	0.850	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCC(=O)O`
ZINC2113934076	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCC(=O)O`
ZINC2113934082	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCC(=O)O`
ZINC2113934083	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCC(=O)O`
ZINC2243670	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCC(=O)O`
ZINC2569203	0.850	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCC(=O)O`
ZINC4798470	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC5973005	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCC(=O)O`
ZINC71418182	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)CCCCC(=O)O`
ZINC79244776	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCCC(=O)O`
ZINC86037082	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCCC(=O)O`
ZINC86037089	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCCCC(=O)O`
ZINC86039283	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCC(=O)O`
ZINC3160730	0.810	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCC(=O)O`
ZINC4582907	0.810	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCC(=O)O`
ZINC4727003	0.810	312.4 Da LogP 4.69 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCC(=O)CCCCCCCC(=O)O`
ZINC86037074	0.810	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)CCCC(=O)O`
ZINC2378801	0.800	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCC(=O)O`
ZINC1556261	0.769	242.3 Da LogP 2.98 TPSA 46.5	✓ Ro5	✓ Clean	`COc1ccc(Cc2ccc(C(=O)O)cc2)cc1`
ZINC39238945	0.769	272.3 Da LogP 2.61 TPSA 72.8	✓ Ro5	✓ Clean	`COc1ccc(C(=O)Oc2ccc(C(=O)O)cc2)cc1`
ZINC9195331	0.769	270.3 Da LogP 3.72 TPSA 46.5	✓ Ro5	✓ Clean	`COc1ccc(C(C)(C)c2ccc(C(=O)O)cc2)cc1`
ZINC2113934081	0.762	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCCCC(=O)O`
ZINC2243668	0.762	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCC(=O)O`
ZINC2378799	0.762	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCC(=O)O`
ZINC33820423	0.762	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCC(=O)O`
ZINC1675842	0.741	292.3 Da LogP 2.23 TPSA 80.7	✓ Ro5	✓ Clean	`COc1ccc(S(=O)(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC2387442	0.739	246.4 Da LogP 4.34 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCSCCCCC(=O)O`
ZINC31778284	0.739	310.4 Da LogP 4.47 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)/C=C\C(=O)CCCCCCCC(=O)O`
ZINC5540108	0.739	310.4 Da LogP 4.47 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)/C=C/C(=O)CCCCCCCC(=O)O`
ZINC64633397	0.739	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCC(=O)O`
ZINC128920	0.731	202.2 Da LogP 2.55 TPSA 46.5	✓ Ro5	✓ Clean	`COc1ccc2cc(C(=O)O)ccc2c1`
ZINC1566855	0.727	270.3 Da LogP 2.77 TPSA 52.6	✓ Ro5	Alert	`COc1ccc(C(=O)C(=O)c2ccc(OC)cc2)cc1`
ZINC59545317	0.727	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCC(=O)O`
ZINC59545320	0.727	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)CCC(=O)O`
ZINC59545336	0.727	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCC(=O)O`
ZINC397461	0.714	286.3 Da LogP 3.04 TPSA 87.7	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)Nc2ccc(C(=O)O)cc2)cc1`
ZINC100292624	0.708	344.4 Da LogP 2.63 TPSA 111.9	✓ Ro5	✓ Clean	`CCCCCCC(=O)[C@@H](O)[C@H](O)C(=O)CCCCCCCC(=O)O`
ZINC117423079	0.708	230.3 Da LogP 3.35 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCC[C@H](O)CCCCC(=O)O`
ZINC59200967	0.708	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCC[C@H](O)CCCCCCCC(=O)O`
ZINC85857782	0.708	286.5 Da LogP 4.91 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCC[C@@H](O)CCCCCCC(=O)O`
ZINC85858219	0.708	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@H](O)CCCCC(=O)O`

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.