Protein profile

VK055_2309

L-2-hydroxyglutarate oxidase

Genome: KpATCC43816

Gene: AIK80913.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GN47

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Amino acids 422

Annotations 8

Features 10

PDB binders 11

Druggability 0.999

Overview

Basic information about this protein and its source genome.

Accession: VK055_2309
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK80913.1
Status: annotated
Amino acids: 422
Structure source: AlphaFold + ColabFold

1.1.5.13

GO:0047545 Catalysis of the reaction: (S)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor. GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0140696 Catalysis of the reaction: (S)-2-hydroxyglutarate + a quinone = 2-oxoglutarate + a quinol. 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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 41.88
Human E-value: 1.92e-25
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 92.33

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 0.999

Structure A0A0H3GN47

Pocket Pocket 1

P2Rank 0.982

Structure A0A0H3GN47

Pocket Pocket 1

ColabFold model

FPocket 0.934 · Pocket 16

P2Rank 0.987 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 44 / 4744 genomes with a hit

Normalized 0.009

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1.1.5.13

Gene Ontology (GO)

GO:0047545 Catalysis of the reaction: (S)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor.
GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0140696 Catalysis of the reaction: (S)-2-hydroxyglutarate + a quinone = 2-oxoglutarate + a quinol.
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:0019477 The chemical reactions and pathways resulting in the breakdown of L-lysine.

Sequence Features

Domain/signature hits from InterPro and related databases.

10 records

Show feature table

Start	End	DB	Term	Name
2	394	PANTHER	PTHR43104	L-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL
86	352	Gene3D	G3DSA:3.30.9.10	-
1	422	Hamap	MF_00990	L-2-hydroxyglutarate dehydrogenase [lhgD].
1	422	InterPro	IPR030862	L-2-hydroxyglutarate dehydrogenase, bacteria
3	390	Pfam	PF01266	FAD dependent oxidoreductase
3	390	InterPro	IPR006076	FAD dependent oxidoreductase
1	285	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
1	285	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
3	386	Gene3D	G3DSA:3.50.50.60	-
3	386	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_A0A0H3GN47	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_2309	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				0.999
22				0.931

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	22.36	0.88
2	10.67	0.573
3	6.43	0.324
4	5.19	0.24
5	2.92	0.093

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
16				0.934
1				0.91

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	39.12	0.961
2	7.37	0.385
3	3.7	0.14
4	3.31	0.116
5	3.25	0.113

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.

61 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
DMG	1EL5	P40859	103.1 Da LogP -0.37 TPSA 40.5	✓ Ro5	✓ Clean	`CN(C)CC(=O)O`
FCG	2A89	P40859	847.7 Da LogP -2.89 TPSA 370.4	3 viol.	✓ Clean	`Cc1cc2c(cc1C)[N@]3[C@@H](CC[C@@]34C(N2C[C@@H]([…`
FOA	2GF3	P40859	112.1 Da LogP 0.98 TPSA 50.4	✓ Ro5	✓ Clean	`c1cc(oc1)C(=O)O`
MSF	1EL8	P40859	152.0 Da LogP -1.09 TPSA 40.1	✓ Ro5	✓ Clean	`C[Se]CC(=O)[O-]`
MTD	1EL7	P40859	200.7 Da LogP -1.09 TPSA 40.1	✓ Ro5	✓ Clean	`C[Te]CC(=O)[O-]`
MTG	1EL9	P40859	105.1 Da LogP -0.90 TPSA 40.1	✓ Ro5	✓ Clean	`CSCC(=O)[O-]`
PYC	1ELI	P40859	110.1 Da LogP -0.62 TPSA 55.9	✓ Ro5	✓ Clean	`c1cc([nH]c1)C(=O)[O-]`
SAR	3QSE	P40859	89.1 Da LogP -0.71 TPSA 49.3	✓ Ro5	✓ Clean	`CNCC(=O)O`
TE	1EL7	P40859	129.6 Da LogP -0.92 TPSA 0.0	✓ Ro5	✓ Clean	`[TeH2]`
THG	4PAA	Q63342	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@H]2C…`
TLA	3DME	Q7VU70	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@@H]([C@H](C(=O)O)O)(C(=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).

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
ZINC4228235	1.000	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@@H](…`
ZINC4228236	1.000	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@H](C…`
ZINC4228237	1.000	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@@H]…`
ZINC4228238	1.000	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@H](…`
ZINC8618631	0.848	459.5 Da LogP 0.11 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CCNc1ccc(C(=O)N[C@@H]…`
ZINC8627114	0.848	459.5 Da LogP 0.11 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CCNc1ccc(C(=O)N[C@@H…`
ZINC4228247	0.712	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CN(C=O)c1ccc(C(=O)N[C…`
ZINC2005305	0.708	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…`
ZINC2572666	0.708	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@@…`
ZINC4228266	0.708	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…`
ZINC4228267	0.708	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@H…`
ZINC12359024	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC13533920	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC1532740	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC1549593	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC2013424	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC3581021	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC3860635	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O`
ZINC5783661	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC6072527	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC9212425	0.689	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…`
ZINC9212426	0.689	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…`
ZINC9212427	0.689	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…`
ZINC9212428	0.689	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…`
ZINC85394426	0.667	206.2 Da LogP 1.80 TPSA 80.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccco2)o1`
ZINC8618632	0.635	459.5 Da LogP 0.52 TPSA 211.8	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@@H](CCNc1ccc(C(=O)N[C@H](CC…`
ZINC8627115	0.635	459.5 Da LogP 0.52 TPSA 211.8	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@H](CCNc1ccc(C(=O)N[C@H](CCC…`
ZINC4228265	0.630	443.4 Da LogP 0.01 TPSA 211.9	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N=C(CNc1ccc(C(=O)N[C@@H](CCC…`
ZINC4517559	0.630	443.4 Da LogP 0.01 TPSA 211.9	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N=C(CNc1ccc(C(=O)N[C@H](CCC(…`
ZINC12374887	0.630	216.2 Da LogP 2.21 TPSA 67.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccco2)cc1`
ZINC8655682	0.628	487.5 Da LogP -0.34 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CCNc1ccc(C(=O)N…`
ZINC2168275	0.619	203.2 Da LogP -2.48 TPSA 107.5	✓ Ro5	✓ Clean	`CNCC(=O)NCC(=O)NCC(=O)O`
ZINC13887836	0.616	429.4 Da LogP 0.54 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)[C@@H](CCc1ccc(C(=O)N[C@@H](…`
ZINC1710770	0.615	200.2 Da LogP 2.35 TPSA 47.3	✓ Ro5	Alert	`O=C(C(=O)c1ccco1)c1ccccc1`
ZINC4658141	0.608	443.5 Da LogP 0.62 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)C[C@H](CCc1ccc(C(=O)N[C@H](C…`
ZINC4658144	0.608	443.5 Da LogP 0.62 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)C[C@@H](CCc1ccc(C(=O)N[C@H](…`
ZINC1613560	0.607	216.2 Da LogP 2.21 TPSA 67.5	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1ccco1`
ZINC4228269	0.605	456.4 Da LogP -0.61 TPSA 193.7	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)[N+]1=CN(c3ccc(C(=O)N[C@@H](…`
ZINC4228270	0.605	456.4 Da LogP -0.61 TPSA 193.7	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)[N+]1=CN(c3ccc(C(=O)N[C@@H](…`
ZINC100477623	0.600	204.2 Da LogP 2.33 TPSA 60.4	✓ Ro5	✓ Clean	`O=C(CC(=O)c1ccco1)c1ccco1`
ZINC6472822	0.600	218.2 Da LogP 2.72 TPSA 60.4	✓ Ro5	✓ Clean	`O=C(CCC(=O)c1ccco1)c1ccco1`
ZINC156403	0.593	274.3 Da LogP 1.47 TPSA 66.9	✓ Ro5	✓ Clean	`O=C(c1ccco1)N1CCN(C(=O)c2ccco2)CC1`
ZINC4654270	0.592	471.4 Da LogP -0.36 TPSA 211.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1C(=O)N(c3ccc(C(=O)N[C@@H](…`
ZINC4654271	0.592	471.4 Da LogP -0.36 TPSA 211.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1C(=O)N(c3ccc(C(=O)N[C@@H](…`
ZINC13515262	0.589	439.4 Da LogP 1.17 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc2ccc(CNc3ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)…`
ZINC1560405156	0.588	208.1 Da LogP -1.79 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)/C(O)=C(\O)[C@H](O)[C@H](O)C(=O)O`
ZINC1560405157	0.588	208.1 Da LogP -1.79 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)/C(O)=C(/O)[C@H](O)[C@H](O)C(=O)O`
ZINC4228243	0.584	457.4 Da LogP -0.52 TPSA 194.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1CN(c3ccc(C(=O)N[C@@H](CCC(…`
ZINC4228244	0.584	457.4 Da LogP -0.52 TPSA 194.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1CN(c3ccc(C(=O)N[C@H](CCC(=…`
ZINC4654260	0.584	457.4 Da LogP -0.52 TPSA 194.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1CN(c3ccc(C(=O)N[C@@H](CCC(…`

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.