Protein profile

KP13_02451

Glyoxylate/hydroxypyruvate reductase A

Genome: KpKP13

Gene: AHE43113.1 Structure source: AlphaFold + ColabFold UniProt A0A2L1BV44

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Amino acids 310

Annotations 4

Features 11

PDB binders 5

Druggability 0.3

Overview

Basic information about this protein and its source genome.

Accession: KP13_02451
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43113.1
Status: annotated
Amino acids: 310
Structure source: AlphaFold + ColabFold

1.1.1.79

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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0030267 Catalysis of the reaction: glycolate + NADP+ = glyoxylate + NADPH + H+.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 29.282
Human E-value: 3.27e-06
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 40.278
DEG E-value: 8.63e-64
Localization: Cytoplasmic
ColabFold pLDDT: 97.17

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 0.3

Structure A0A2L1BV44

Pocket Pocket 14

P2Rank 0.956

Structure A0A2L1BV44

Pocket Pocket 1

ColabFold model

FPocket 0.871 · Pocket 7

P2Rank 0.964 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 10 / 4744 genomes with a hit

Normalized 0.002

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

1.1.1.79

Gene Ontology (GO)

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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0030267 Catalysis of the reaction: glycolate + NADP+ = glyoxylate + NADPH + H+.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records

Show feature table

Start	End	DB	Term	Name
94	276	Gene3D	G3DSA:3.40.50.720	-
95	276	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
95	276	InterPro	IPR036291	NAD(P)-binding domain superfamily
4	305	CDD	cd12164	GDH_like_2
214	230	ProSitePatterns	PS00671	D-isomer specific 2-hydroxyacid dehydrogenases signature 3.
214	230	InterPro	IPR029753	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site
23	302	Gene3D	G3DSA:3.40.50.720	-
52	310	PANTHER	PTHR43333	2-HACID_DH_C DOMAIN-CONTAINING PROTEIN
35	92	SUPERFAMILY	SSF52283	Formate/glycerate dehydrogenase catalytic domain-like
104	275	Pfam	PF02826	D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
104	275	InterPro	IPR006140	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain

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_A0A2L1BV44	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02451	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				0.3
1				0.241
11				0.239

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				24.77	0.901
2				3.62	0.135

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
7				0.871

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				31.45	0.939

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
7N5	5MH5	Q2VEQ7	130.1 Da LogP 0.83 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)C(=O)O`
GLV	6OXN	P75913	74.0 Da LogP -0.73 TPSA 54.4	✓ Ro5	✓ Clean	`C(=O)C(=O)O`
OXD	5TSD	Q2KDT2	90.0 Da LogP -0.84 TPSA 74.6	✓ Ro5	✓ Clean	`C(=O)(C(=O)O)O`
PE4	4N18	B5XVG7	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
TLA	5BQF	Q2KDT2	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
ZINC5650743	1.000	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917	1.000	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
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`
ZINC12501520	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716	0.688	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	0.688	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	0.688	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	0.688	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	0.688	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5859031	0.688	294.4 Da LogP 1.13 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCC`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC14686440	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC1644613	0.619	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC1580161	0.600	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.600	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.600	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	0.600	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	0.600	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.600	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860	0.600	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC2555269	0.591	220.3 Da LogP 1.22 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCOCCOCCOCCO`
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`
ZINC4974293	0.579	280.4 Da LogP 1.08 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCOCCOCCOCC`
ZINC13398039	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC2528012	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC1672455	0.571	226.4 Da LogP 4.07 TPSA 34.1	✓ Ro5	Alert	`CCCCCCC(=O)C(=O)CCCCCC`
ZINC100070166	0.565	290.4 Da LogP 3.17 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCO`
ZINC100365196	0.565	302.5 Da LogP 4.71 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCO`
ZINC101772322	0.565	434.7 Da LogP 4.76 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC14881140	0.565	306.4 Da LogP 2.41 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCO`
ZINC16051619	0.565	350.5 Da LogP 2.42 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCOCCO`
ZINC59441819	0.565	318.5 Da LogP 3.95 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCO`
ZINC59622400	0.565	274.4 Da LogP 3.93 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCO`
ZINC71788551	0.565	334.5 Da LogP 3.19 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCO`
ZINC71788564	0.565	262.4 Da LogP 2.39 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCO`
ZINC95784968	0.565	450.7 Da LogP 4.00 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`

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.