Protein profile

KP13_00254

Glyoxylate/hydroxypyruvate reductase B

Genome: KpKP13

Gene: ghrB AHE42166.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GYP5

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Amino acids 323

Annotations 10

Features 18

PDB binders 5

Druggability 0.427

Overview

Basic information about this protein and its source genome.

Accession: KP13_00254
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: ghrB AHE42166.1
Status: annotated
Amino acids: 323
Structure source: AlphaFold + ColabFold

1.1.1.79 1.1.1.81

GO:0016618 Catalysis of the reaction: (R)-glycerate + NAD(P)+ = 3-hydroxypyruvate + NAD(P)H + H+. GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH. GO:0030267 Catalysis of the reaction: glycolate + NADP+ = glyoxylate + NADPH + H+. GO:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 40.206
Human E-value: 3.45e-58
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 97.35

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 0.427

Structure A0A0H3GYP5

Pocket Pocket 14

P2Rank 0.88

Structure A0A0H3GYP5

Pocket Pocket 1

ColabFold model

FPocket 0.431 · Pocket 15

P2Rank 0.877 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 123 / 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.

2 EC 8 GO

Enzyme Commission (EC)

Gene Ontology (GO)

GO:0016618 Catalysis of the reaction: (R)-glycerate + NAD(P)+ = 3-hydroxypyruvate + NAD(P)H + H+.
GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
GO:0030267 Catalysis of the reaction: glycolate + NADP+ = glyoxylate + NADPH + H+.
GO:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
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:0008465 Catalysis of the reaction: (R)-glycerate + NAD+ = 3-hydroxypyruvate + NADH + H+.
GO:0120509 Catalysis of the reaction: (R)-glycerate + NADP+ = 3-hydroxypyruvate + NADPH + H+.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
100	288	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
100	288	InterPro	IPR036291	NAD(P)-binding domain superfamily
226	242	ProSitePatterns	PS00671	D-isomer specific 2-hydroxyacid dehydrogenases signature 3.
226	242	InterPro	IPR029753	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site
98	286	FunFam	G3DSA:3.40.50.720:FF:000026	Glyoxylate/hydroxypyruvate reductase B
1	134	SUPERFAMILY	SSF52283	Formate/glycerate dehydrogenase catalytic domain-like
3	311	CDD	cd05301	GDH
6	311	Gene3D	G3DSA:3.40.50.720	-
18	311	PANTHER	PTHR10996	2-HYDROXYACID DEHYDROGENASE-RELATED
197	219	ProSitePatterns	PS00670	D-isomer specific 2-hydroxyacid dehydrogenases signature 2.
197	219	InterPro	IPR029753	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site
108	287	Pfam	PF02826	D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
108	287	InterPro	IPR006140	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain
5	319	Pfam	PF00389	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
5	319	InterPro	IPR006139	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
98	286	Gene3D	G3DSA:3.40.50.720	-
1	323	Hamap	MF_01667	Glyoxylate/hydroxypyruvate reductase B [ghrB].
1	323	InterPro	IPR023756	Glyoxylate/hydroxypyruvate reductase B

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_A0A0H3GYP5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00254	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
14				0.427

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				14.49	0.724

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
15				0.431
16				0.318

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				14.33	0.719
2				1.68	0.029

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.

55 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
A7R	6IH3	G4XDR8	640.4 Da LogP -3.60 TPSA 309.5	3 viol.	✓ Clean	`c1cc(c[n+](c1)[C@@H]2[C@@H]([C@@H]([C@@H](O2)CO…`
DGY	2GCG	Q9UBQ7	106.1 Da LogP -1.58 TPSA 77.8	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)O)O`
GLV	5AOV	Q8U3Y2	74.0 Da LogP -0.73 TPSA 54.4	✓ Ro5	✓ Clean	`C(=O)C(=O)O`
MLI	6BII	F8AEA4	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
NHE	2CUK	Q5SMG6	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCS(=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
ZINC1710230	1.000	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
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`
ZINC12502055	0.667	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC12502057	0.667	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC12502058	0.667	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC13431057	0.667	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC13431059	0.667	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC25726736	0.667	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC3861746	0.667	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@@](=O)(O)…`
ZINC53683723	0.667	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC82142138	0.667	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC82142140	0.667	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC104864216	0.662	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@](=O)(O)OP(=O)(O)O)[C…`
ZINC12504412	0.662	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC12504413	0.662	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC12504414	0.662	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC13431045	0.662	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC13431047	0.662	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC13548733	0.662	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC33913782	0.662	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC8215624	0.662	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC8216134	0.647	446.2 Da LogP -2.35 TPSA 238.9	2 viol.	✓ Clean	`NCCO[P@@](=O)(O)O[P@](=O)(O)OC[C@H]1O[C@@H](n2c…`
ZINC12503278	0.615	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…`
ZINC1532667	0.615	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@H]2O[C@@H](COP(=O)(O)O)[C@H]…`
ZINC2545161	0.615	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@@H](COP(=O)(O)O)[C@H…`
ZINC3870109	0.615	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@@H](COP(=O)(O)O)[C@@…`
ZINC40465856	0.615	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…`
ZINC40762833	0.615	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@H]2O[C@H](COP(=O)(O)O)[C@@H]…`
ZINC4228273	0.615	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…`
ZINC77311638	0.615	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…`
ZINC146373408	0.612	337.2 Da LogP -1.79 TPSA 166.4	✓ Ro5	✓ Clean	`CO[P@](=O)(O)OC[C@@H]1O[C@H](n2ccc(N)nc2=O)[C@H…`
ZINC36471998	0.612	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(OP(=O)(O)O)OP(=O)(…`
ZINC101145080	0.611	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC106404522	0.611	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC12660526	0.611	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…`
ZINC16696677	0.611	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1O…`
ZINC215821427	0.611	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC36382611	0.611	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…`
ZINC5048329	0.611	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@](=O)(O)OC[C@H]1O…`
ZINC6507065	0.611	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…`
ZINC8216074	0.611	477.3 Da LogP -2.95 TPSA 253.3	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@](=O)(O)…`
ZINC8551188	0.611	477.3 Da LogP -2.95 TPSA 253.3	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)(O)O…`
ZINC9211548	0.611	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1O…`
ZINC96023557	0.611	489.3 Da LogP -1.60 TPSA 212.9	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…`
ZINC1532524	0.600	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@@H]…`
ZINC16546001	0.600	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@@H]…`
ZINC3954230	0.600	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H]2…`
ZINC8613159	0.600	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@H]2…`
ZINC8952080	0.600	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@@H…`

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.