Protein profile

KP13_05588

D-lactate dehydrogenase

Genome: KpKP13

Gene: AHE44872.1 ldhA Structure source: AlphaFold + ColabFold UniProt A0A0H3GWL1

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Amino acids 329

Annotations 4

Features 18

PDB binders 7

Druggability 0.592

Overview

Basic information about this protein and its source genome.

Accession: KP13_05588
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44872.1 ldhA
Status: annotated
Amino acids: 329
Structure source: AlphaFold + ColabFold

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: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:0008720 Catalysis of the reaction: (R)-lactate + NAD+ = H+ + NADH + pyruvate.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 40.984
Human E-value: 7.839999999999999e-23
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 70.517
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 95.24

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 0.592

Structure A0A0H3GWL1

Pocket Pocket 21

P2Rank 0.314

Structure A0A0H3GWL1

Pocket Pocket 1

ColabFold model

FPocket 0.651 · Pocket 18

P2Rank 0.777 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 535 / 4744 genomes with a hit

Normalized 0.113

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

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: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:0008720 Catalysis of the reaction: (R)-lactate + NAD+ = H+ + NADH + pyruvate.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
1	329	PANTHER	PTHR43026	2-HYDROXYACID DEHYDROGENASE HOMOLOG 1-RELATED
102	297	FunFam	G3DSA:3.40.50.720:FF:000050	D-lactate dehydrogenase
110	297	Pfam	PF02826	D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
110	297	InterPro	IPR006140	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain
194	216	ProSitePatterns	PS00670	D-isomer specific 2-hydroxyacid dehydrogenases signature 2.
194	216	InterPro	IPR029753	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site
2	135	SUPERFAMILY	SSF52283	Formate/glycerate dehydrogenase catalytic domain-like
102	297	Gene3D	G3DSA:3.40.50.720	-
6	318	Gene3D	G3DSA:3.40.50.720	-
3	328	Pfam	PF00389	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
3	328	InterPro	IPR006139	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
147	174	ProSitePatterns	PS00065	D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.
147	174	InterPro	IPR029752	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1
223	239	ProSitePatterns	PS00671	D-isomer specific 2-hydroxyacid dehydrogenases signature 3.
223	239	InterPro	IPR029753	D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site
1	328	CDD	cd12183	LDH_like_2
102	298	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
102	298	InterPro	IPR036291	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_A0A0H3GWL1	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05588	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
21				0.592
3				0.018
15				0.001
7				0.0

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	7.2	0.314
2	6.5	0.276
3	6.01	0.245
4	3.19	0.087
5	2.71	0.066

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
18				0.651

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	15.18	0.748
2	2.72	0.081
3	2.16	0.051
4	2.08	0.047

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.

66 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
3CR	4U6Q	Q13363	179.2 Da LogP 1.14 TPSA 69.9	✓ Ro5	✓ Clean	`c1ccc(cc1)C/C(=N\O)/C(=O)O`
GLV	5AOV	Q8U3Y2	74.0 Da LogP -0.73 TPSA 54.4	✓ Ro5	✓ Clean	`C(=O)C(=O)O`
KMT	4LCE	Q13363	148.2 Da LogP 0.39 TPSA 54.4	✓ Ro5	✓ Clean	`CSCCC(=O)C(=O)O`
LAC	3KB6	O66939	90.1 Da LogP -0.55 TPSA 57.5	✓ Ro5	✓ Clean	`C[C@H](C(=O)O)O`
MLI	6BII	F8AEA4	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
PPI	3KB6	O66939	74.1 Da LogP 0.48 TPSA 37.3	✓ Ro5	✓ Clean	`CCC(=O)O`
PPY	4U6S	Q13363	164.2 Da LogP 0.88 TPSA 54.4	✓ Ro5	✓ Clean	`c1ccc(cc1)CC(=O)C(=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL3799940	P56545	6.77	213.6 Da LogP 1.80 TPSA 69.9	✓ Ro5	✓ Clean	`O=C(O)/C(Cc1cccc(Cl)c1)=N\O`
CHEMBL3798669	P56545	6.75	213.6 Da LogP 1.80 TPSA 69.9	✓ Ro5	✓ Clean	`O=C(O)/C(Cc1ccc(Cl)cc1)=N\O`
CHEMBL3797778	P56545	6.62	179.2 Da LogP 1.14 TPSA 69.9	✓ Ro5	✓ Clean	`O=C(O)/C(Cc1ccccc1)=N\O`
CHEMBL3800609	P56545	6.52	197.2 Da LogP 1.28 TPSA 69.9	✓ Ro5	✓ Clean	`O=C(O)/C(Cc1ccc(F)cc1)=N\O`
CHEMBL3800006	P56545	6.50	193.2 Da LogP 1.45 TPSA 69.9	✓ Ro5	✓ Clean	`Cc1ccc(C/C(=N/O)C(=O)O)cc1`
CHEMBL3800187	P56545	6.32	193.2 Da LogP 1.45 TPSA 69.9	✓ Ro5	✓ Clean	`Cc1cccc(C/C(=N/O)C(=O)O)c1`
CHEMBL3799689	P56545	6.14	195.2 Da LogP 0.85 TPSA 90.1	✓ Ro5	✓ Clean	`O=C(O)/C(Cc1cccc(O)c1)=N\O`
CHEMBL3799251	P56545	6.06	209.2 Da LogP 1.15 TPSA 79.1	✓ Ro5	✓ Clean	`COc1cccc(C/C(=N/O)C(=O)O)c1`
CHEMBL3797935	P56545	6.05	204.2 Da LogP 1.02 TPSA 93.7	✓ Ro5	✓ Clean	`N#Cc1ccc(C/C(=N/O)C(=O)O)cc1`

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
ZINC1602735	0.800	238.3 Da LogP 2.61 TPSA 34.1	✓ Ro5	Alert	`O=C(Cc1ccccc1)C(=O)Cc1ccccc1`
ZINC100369423	0.750	268.3 Da LogP 3.13 TPSA 65.2	✓ Ro5	Alert	`O/N=C(Cc1ccccc1)/C(Cc1ccccc1)=N/O`
ZINC17315900	0.750	268.3 Da LogP 3.13 TPSA 65.2	✓ Ro5	Alert	`O/N=C(Cc1ccccc1)\C(Cc1ccccc1)=N\O`
ZINC22219569	0.750	240.3 Da LogP 2.55 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)C(=O)Cc1ccc(-c2ccccc2)cc1`
ZINC250824491	0.750	268.3 Da LogP 3.13 TPSA 65.2	✓ Ro5	Alert	`ON=C(Cc1ccccc1)/C(Cc1ccccc1)=N/O`
ZINC384195530	0.677	213.6 Da LogP 1.80 TPSA 69.9	✓ Ro5	✓ Clean	`O=C(O)C(Cc1cccc(Cl)c1)=NO`
ZINC6580259	0.655	270.3 Da LogP 2.46 TPSA 63.6	✓ Ro5	✓ Clean	`O=C(O)C(=O)Cc1ccc(OCc2ccccc2)cc1`
ZINC19256938	0.640	243.1 Da LogP 1.65 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)C(=O)Cc1ccc(Br)cc1`
ZINC1679978	0.636	210.3 Da LogP 3.04 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(Cc1ccccc1)Cc1ccccc1`
ZINC19862918	0.633	205.2 Da LogP 1.30 TPSA 66.7	✓ Ro5	✓ Clean	`CC(=O)/N=C(/Cc1ccccc1)C(=O)O`
ZINC13398595	0.625	209.2 Da LogP 1.15 TPSA 79.1	✓ Ro5	✓ Clean	`COc1ccc(C/C(=N\O)C(=O)O)cc1`
ZINC4532445	0.625	209.2 Da LogP 1.15 TPSA 79.1	✓ Ro5	✓ Clean	`COc1ccc(C/C(=N/O)C(=O)O)cc1`
ZINC22221925	0.607	243.1 Da LogP 1.65 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)C(=O)Cc1cccc(Br)c1`
ZINC5521335	0.607	214.2 Da LogP 2.04 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)C(=O)Cc1ccc2ccccc2c1`
ZINC104374849	0.606	207.2 Da LogP 1.62 TPSA 58.9	✓ Ro5	✓ Clean	`CCOC(=O)/C(Cc1ccccc1)=N/O`
ZINC14619979	0.606	207.2 Da LogP 1.62 TPSA 58.9	✓ Ro5	✓ Clean	`CCOC(=O)/C(Cc1ccccc1)=N\O`
ZINC22910924	0.606	224.2 Da LogP 1.05 TPSA 113.0	✓ Ro5	✓ Clean	`O=C(O)/C(Cc1ccc([N+](=O)[O-])cc1)=N\O`
ZINC7995844	0.606	224.2 Da LogP 1.05 TPSA 113.0	✓ Ro5	✓ Clean	`O=C(O)/C(Cc1ccc([N+](=O)[O-])cc1)=N/O`
ZINC19256010	0.600	256.3 Da LogP 2.68 TPSA 63.6	✓ Ro5	✓ Clean	`O=C(O)C(=O)Cc1cccc(Oc2ccccc2)c1`
ZINC2565500	0.600	226.3 Da LogP 3.12 TPSA 26.3	✓ Ro5	✓ Clean	`COc1cccc(CC(=O)c2ccccc2)c1`
ZINC263622944	0.600	208.2 Da LogP 1.28 TPSA 63.6	✓ Ro5	✓ Clean	`COc1cccc(CC(=O)CC(=O)O)c1`
ZINC22211451	0.593	220.3 Da LogP 2.18 TPSA 54.4	✓ Ro5	✓ Clean	`CC(C)(C)c1ccc(CC(=O)C(=O)O)cc1`
ZINC3845185	0.586	266.3 Da LogP 0.88 TPSA 91.7	✓ Ro5	Alert	`O=C(O)C(=O)Cc1cccc(CC(=S)C(=O)O)c1`
ZINC102854104	0.585	271.3 Da LogP 3.12 TPSA 51.0	✓ Ro5	✓ Clean	`COc1cccc(C/C(=N/O)c2cccc(OC)c2)c1`
ZINC16970765	0.585	271.3 Da LogP 3.12 TPSA 51.0	✓ Ro5	✓ Clean	`COc1cccc(C/C(=N\O)c2cccc(OC)c2)c1`
ZINC1640929	0.583	253.3 Da LogP 2.11 TPSA 46.2	✓ Ro5	✓ Clean	`O=C(Cc1ccccc1)NC(=O)Cc1ccccc1`
ZINC137507	0.577	225.3 Da LogP 3.30 TPSA 32.6	✓ Ro5	✓ Clean	`ON=C(Cc1ccccc1)Cc1ccccc1`
ZINC1646626	0.571	209.2 Da LogP 0.79 TPSA 97.5	✓ Ro5	✓ Clean	`O=C(O)C(=O)Cc1ccc([N+](=O)[O-])cc1`
ZINC19260933	0.571	232.2 Da LogP 1.90 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)C(=O)Cc1ccc(C(F)(F)F)cc1`
ZINC26544403	0.571	237.3 Da LogP 2.85 TPSA 61.1	✓ Ro5	✓ Clean	`N#Cc1ccc(-c2ccc(CC(=O)O)cc2)cc1`
ZINC3481043	0.571	241.3 Da LogP 2.88 TPSA 38.3	✓ Ro5	✓ Clean	`COc1cccc(CC(=O)Nc2ccccc2)c1`
ZINC2518009	0.561	218.2 Da LogP 2.37 TPSA 26.3	✓ Ro5	✓ Clean	`COc1cccc(CC(=O)C(F)(F)F)c1`
ZINC2581007	0.561	242.3 Da LogP 2.99 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cccc(-c2cccc(CC(=O)O)c2)c1`
ZINC35316373	0.561	222.2 Da LogP 1.37 TPSA 52.6	✓ Ro5	✓ Clean	`COC(=O)CC(=O)Cc1cccc(OC)c1`
ZINC41217189	0.561	208.3 Da LogP 2.35 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cccc(CC(C)(C)C(=O)O)c1`
ZINC46346384	0.561	207.3 Da LogP 1.76 TPSA 38.3	✓ Ro5	✓ Clean	`COc1cccc(CC(=O)NC(C)C)c1`
ZINC7007755	0.561	285.3 Da LogP 2.56 TPSA 47.6	✓ Ro5	✓ Clean	`COc1cccc(CNC(=O)Cc2cccc(OC)c2)c1`
ZINC1764694	0.560	270.4 Da LogP 3.26 TPSA 34.1	✓ Ro5	✓ Clean	`O=C(Cc1ccccc1)SC(=O)Cc1ccccc1`
ZINC3181003	0.560	314.4 Da LogP 4.54 TPSA 34.1	✓ Ro5	✓ Clean	`O=C(Cc1ccccc1)c1ccc(C(=O)Cc2ccccc2)cc1`
ZINC102912914	0.556	282.3 Da LogP 2.94 TPSA 61.7	✓ Ro5	✓ Clean	`C[C@H](NC(=O)/C(Cc1ccccc1)=N\O)c1ccccc1`
ZINC102912916	0.556	282.3 Da LogP 2.94 TPSA 61.7	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)/C(Cc1ccccc1)=N\O)c1ccccc1`
ZINC1560407661	0.556	207.2 Da LogP 1.36 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)C[C](Cc1ccccc1)C(=O)O`
ZINC17430172	0.556	282.3 Da LogP 2.94 TPSA 61.7	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)/C(Cc1ccccc1)=N/O)c1ccccc1`
ZINC17430176	0.556	282.3 Da LogP 2.94 TPSA 61.7	✓ Ro5	✓ Clean	`C[C@H](NC(=O)/C(Cc1ccccc1)=N/O)c1ccccc1`
ZINC19435375	0.556	243.1 Da LogP 1.65 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)C(=O)Cc1ccccc1Br`
ZINC33466492	0.552	238.3 Da LogP 3.66 TPSA 17.1	✓ Ro5	✓ Clean	`Cc1ccc(CC(=O)Cc2ccc(C)cc2)cc1`
ZINC19255855	0.548	232.2 Da LogP 1.90 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)C(=O)Cc1cccc(C(F)(F)F)c1`
ZINC4898998	0.548	207.2 Da LogP 1.92 TPSA 69.9	✓ Ro5	✓ Clean	`O=C(O)CC/C(Cc1ccccc1)=N\O`
ZINC3607673	0.548	271.3 Da LogP 2.89 TPSA 47.6	✓ Ro5	✓ Clean	`COc1cccc(CC(=O)Nc2cccc(OC)c2)c1`
ZINC44866950	0.548	221.3 Da LogP 2.11 TPSA 29.5	✓ Ro5	✓ Clean	`CCN(CC)C(=O)Cc1cccc(OC)c1`

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.