Protein profile

KP13_02981

Malate dehydrogenase

Genome: KpKP13

Gene: AHE42438.1 mdh Structure source: AlphaFold + ColabFold UniProt A0A0H3GWA1
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Amino acids 312
Annotations 10
Features 29
PDB binders 4
Druggability 0.863

Overview

Basic information about this protein and its source genome.

Accession
KP13_02981
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42438.1 mdh
Status
annotated
Amino acids
312
Structure source
AlphaFold + ColabFold
EC
1.1.1.37
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:0006108 The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle. GO:0019752 The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-). GO:0030060 Catalysis of the reaction: (S)-malate + NAD+ = oxaloacetate + 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 (%)
59.164
Human E-value
3.23e-119
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
77.814
DEG E-value
1.65e-166
Localization
Unknown
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 0.863
Structure A0A0H3GWA1
Pocket Pocket 4
P2Rank 0.662
Structure A0A0H3GWA1
Pocket Pocket 1
ColabFold model
FPocket 0.781 · Pocket 3
P2Rank 0.603 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 163 / 4744 genomes with a hit
Normalized 0.034

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • 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:0006108 The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.
  • GO:0019752 The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
  • GO:0030060 Catalysis of the reaction: (S)-malate + NAD+ = oxaloacetate + 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:0006099 A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
  • GO:0016615 Catalysis of the reversible conversion of pyruvate or oxaloacetate to malate.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence Features

Domain/signature hits from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
146 158 ProSitePatterns PS00068 Malate dehydrogenase active site signature.
146 158 InterPro IPR001252 Malate dehydrogenase, active site
1 311 Hamap MF_01516 Malate dehydrogenase [mdh].
1 311 InterPro IPR023958 Malate dehydrogenase, type 1, bacterial
1 2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
146 311 SUPERFAMILY SSF56327 LDH C-terminal domain-like
146 311 InterPro IPR015955 Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal
1 310 CDD cd01337 MDH_glyoxysomal_mitochondrial
1 310 InterPro IPR010097 Malate dehydrogenase, type 1
13 17 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
3 12 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 146 Gene3D G3DSA:3.40.50.720 -
1 312 PANTHER PTHR11540 MALATE AND LACTATE DEHYDROGENASE
147 310 Pfam PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal domain
147 310 InterPro IPR022383 Lactate/malate dehydrogenase, C-terminal
2 311 NCBIfam TIGR01772 malate dehydrogenase
2 311 InterPro IPR010097 Malate dehydrogenase, type 1
1 145 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
1 145 InterPro IPR036291 NAD(P)-binding domain superfamily
1 146 FunFam G3DSA:3.40.50.720:FF:000017 Malate dehydrogenase
18 312 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
147 312 FunFam G3DSA:3.90.110.10:FF:000001 Malate dehydrogenase
1 17 Phobius SIGNAL_PEPTIDE Signal peptide region
1 145 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain
1 145 InterPro IPR001236 Lactate/malate dehydrogenase, N-terminal
147 312 Gene3D G3DSA:3.90.110.10 -
147 312 InterPro IPR015955 Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal
1 309 PIRSF PIRSF000102 Lac_mal_DH
1 309 InterPro IPR001557 L-lactate/malate dehydrogenase

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_A0A0H3GWA1
AlphaFold — — full sequence — Viewing
ColabFold KP13_02981
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
4 0.863

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 8.35 0.445
2 5.13 0.236
3 1.01 0.006

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.

54 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
6V0
5KKA
P61889 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)…
LMR
2DFD
P40926 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)O)C(=O)O
OAA
5ZI4
P32419 131.1 Da LogP -2.22 TPSA 94.5 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)C(=O)[O-]
PYR
1IE3
P61889 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.