Protein profile

KP13_05264

L-lactate dehydrogenase 2

Genome: KpKP13

Gene: ldh2 AHE44671.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GN55
Export view
Amino acids 314
Annotations 9
Features 31
PDB binders 10
Druggability 0.568

Overview

Basic information about this protein and its source genome.

Accession
KP13_05264
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
ldh2 AHE44671.1
Status
annotated
Amino acids
314
Structure source
AlphaFold + ColabFold
EC
1.1.1.27
GO
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:0019752 The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-). GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0004459 Catalysis of the reaction: (S)-lactate + NAD+ = pyruvate + NADH + H+. 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:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
34.359
Human E-value
2.64e-36
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.07

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 0.568
Structure A0A0H3GN55
Pocket Pocket 15
P2Rank 0.859
Structure A0A0H3GN55
Pocket Pocket 1
ColabFold model
FPocket 0.455 · Pocket 14
P2Rank 0.893 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 26 / 4744 genomes with a hit
Normalized 0.005

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • 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:0019752 The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0004459 Catalysis of the reaction: (S)-lactate + NAD+ = pyruvate + NADH + H+.
  • 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:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0006096 The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
  • GO:0006089 The chemical reactions and pathways involving lactate, the anion of lactic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
2 313 PIRSF PIRSF000102 Lac_mal_DH
2 313 InterPro IPR001557 L-lactate/malate dehydrogenase
150 313 Gene3D G3DSA:3.90.110.10 -
150 313 InterPro IPR015955 Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal
4 310 PANTHER PTHR43128 L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+))
5 314 Hamap MF_00488 L-lactate dehydrogenase [ldh].
5 314 InterPro IPR011304 L-lactate dehydrogenase
10 307 NCBIfam TIGR01771 L-lactate dehydrogenase
10 307 InterPro IPR011304 L-lactate dehydrogenase
1 148 Gene3D G3DSA:3.40.50.720 -
176 182 ProSitePatterns PS00064 L-lactate dehydrogenase active site.
176 182 InterPro IPR018177 L-lactate dehydrogenase, active site
6 312 CDD cd05291 HicDH_like
3 146 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
3 146 InterPro IPR036291 NAD(P)-binding domain superfamily
7 146 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain
7 146 InterPro IPR001236 Lactate/malate dehydrogenase, N-terminal
151 311 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain
151 311 InterPro IPR022383 Lactate/malate dehydrogenase, C-terminal
144 162 PRINTS PR00086 L-lactate dehydrogenase signature
144 162 InterPro IPR001557 L-lactate/malate dehydrogenase
174 187 PRINTS PR00086 L-lactate dehydrogenase signature
174 187 InterPro IPR001557 L-lactate/malate dehydrogenase
120 140 PRINTS PR00086 L-lactate dehydrogenase signature
120 140 InterPro IPR001557 L-lactate/malate dehydrogenase
32 56 PRINTS PR00086 L-lactate dehydrogenase signature
32 56 InterPro IPR001557 L-lactate/malate dehydrogenase
7 31 PRINTS PR00086 L-lactate dehydrogenase signature
7 31 InterPro IPR001557 L-lactate/malate dehydrogenase
147 311 SUPERFAMILY SSF56327 LDH C-terminal domain-like
147 311 InterPro IPR015955 Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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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_A0A0H3GN55
AlphaFold — — full sequence — Viewing
ColabFold KP13_05264
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
15 0.568
16 0.308

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 13.42 0.686
2 1.73 0.031
3 0.66 0.001

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.

60 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
1E4
4I9H
P13491 748.1 Da LogP 2.97 TPSA 238.1 3 viol. ✓ Clean COc1cc(c(cc1NC(=O)CSc2ccc(cn2)C(=O)O)Cl)OC[C@H]…
1E5
4I9N
P13491 291.2 Da LogP 2.05 TPSA 96.7 ✓ Ro5 ✓ Clean c1cc(ncc1C(=O)O)c2cc(cc(c2)F)OCC(=O)O
1E6
4I9N
P13491 442.9 Da LogP 1.90 TPSA 138.2 ✓ Ro5 ✓ Clean COc1cc(c(cc1NC(=O)CSc2ccc(cn2)C(=O)O)Cl)OC[C@H]…
1E7
4I9U
P13491 352.8 Da LogP 3.17 TPSA 88.5 ✓ Ro5 ✓ Clean COc1ccc(cc1NC(=O)CSc2ccc(cn2)C(=O)O)Cl
6P3
4I8X
P13491 199.2 Da LogP 2.45 TPSA 50.2 ✓ Ro5 ✓ Clean c1ccc(cc1)c2ccc(cn2)C(=O)O
6V0
5KKC
P13491 665.4 Da LogP -3.03 TPSA 317.6 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
APR
7BYA
A0A143T1U9 559.3 Da LogP -3.28 TPSA 291.5 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
MLI
5NQB
P13491 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
OAA
7BY9
A0A143T1U9 131.1 Da LogP -2.22 TPSA 94.5 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)C(=O)[O-]
PYR
6J9U
P00343 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=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.