Protein profile

KP13_03896

putative tartrate dehydrogenase/decarboxylase

Genome: KpKP13

Gene: AHE45358.1 Structure source: AlphaFold + ColabFold UniProt A0A6A8EH95
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Amino acids 365
Annotations 5
Features 11
PDB binders 9
Druggability 0.375

Overview

Basic information about this protein and its source genome.

Accession
KP13_03896
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE45358.1
Status
annotated
Amino acids
365
Structure source
AlphaFold + ColabFold
EC
1.1.1.83
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:0000287 Binding to a magnesium (Mg) ion. 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:0046553 Catalysis of the reaction: (R)-malate + NAD+ = CO2 + NADH + pyruvate.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
41.176
Human E-value
1.3e-09
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
42.903
DEG E-value
1.81e-72
Localization
Cytoplasmic
ColabFold pLDDT
96.82

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 0.375
Structure A0A6A8EH95
Pocket Pocket 10
P2Rank 0.733
Structure A0A6A8EH95
Pocket Pocket 1
ColabFold model
FPocket 0.631 · Pocket 9
P2Rank 0.69 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 139 / 4744 genomes with a hit
Normalized 0.029

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • 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:0000287 Binding to a magnesium (Mg) ion.
  • 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:0046553 Catalysis of the reaction: (R)-malate + NAD+ = CO2 + NADH + pyruvate.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
11 359 Pfam PF00180 Isocitrate/isopropylmalate dehydrogenase
11 359 InterPro IPR024084 Isopropylmalate dehydrogenase-like domain
10 359 SMART SM01329 Iso_dh_2
10 359 InterPro IPR024084 Isopropylmalate dehydrogenase-like domain
248 267 ProSitePatterns PS00470 Isocitrate and isopropylmalate dehydrogenases signature.
248 267 InterPro IPR019818 Isocitrate/isopropylmalate dehydrogenase, conserved site
5 363 SUPERFAMILY SSF53659 Isocitrate/Isopropylmalate dehydrogenase-like
6 363 PANTHER PTHR43275 D-MALATE DEHYDROGENASE [DECARBOXYLATING]
6 363 NCBIfam TIGR02089 tartrate dehydrogenase
6 363 InterPro IPR011829 Tartrate dehydrogenase
5 364 Gene3D G3DSA:3.40.718.10 Isopropylmalate 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_A0A6A8EH95
AlphaFold — — full sequence — Viewing
ColabFold KP13_03896
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
10 0.375
16 0.249

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 14.01 0.708
2 5.96 0.293
3 2.63 0.077
4 1.07 0.007

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.

20 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
48Y
4YB4
Q72IW9 206.1 Da LogP -1.00 TPSA 132.1 ✓ Ro5 ✓ Clean C(CC(=O)O)[C@@H]([C@H](C(=O)O)O)C(=O)O
DEI
2ZTW
Q5SIY4 134.2 Da LogP 0.83 TPSA 57.5 ✓ Ro5 ✓ Clean CS\C=C(\C(=O)O)/O
DTT
3FLK
Q51945 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
IPM
2Y41
Q5SIY4 176.2 Da LogP -0.21 TPSA 94.8 ✓ Ro5 ✓ Clean CC(C)[C@@H]([C@H](C(=O)O)O)C(=O)O
NH4
3FLK
Q51945 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
O45
6XXY
P43860 159.1 Da LogP -0.31 TPSA 75.6 ✓ Ro5 ✓ Clean CC(=C)CONC(=O)C(=O)O
OXL
3FLK
Q51945 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=O)[O-])[O-]
XYM
3ASJ
Q5SIJ1 178.2 Da LogP 0.29 TPSA 94.8 ✓ Ro5 ✓ Clean C(C(=O)O)S/C=C(/C(=O)O)\O
XYN
3ASJ
Q5SIJ1 178.2 Da LogP -0.54 TPSA 91.7 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)SCC(=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.