Protein profile

KP13_04861

Isocitrate dehydrogenase [NADP]

Genome: KpKP13

Gene: AHE45221.1 icd Structure source: AlphaFold + ColabFold UniProt A0A0H3GVN3
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Amino acids 416
Annotations 7
Features 12
PDB binders 11
Druggability 0.449

Overview

Basic information about this protein and its source genome.

Accession
KP13_04861
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE45221.1 icd
Status
annotated
Amino acids
416
Structure source
AlphaFold + ColabFold
EC
1.1.1.42
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:0000287 Binding to a magnesium (Mg) ion. 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: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:0004450 Catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH. GO:0006097 A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
40.741
Human E-value
4.43e-08
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
97.596
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.04

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 0.449
Structure A0A0H3GVN3
Pocket Pocket 1
P2Rank 0.733
Structure A0A0H3GVN3
Pocket Pocket 1
ColabFold model
FPocket 0.083 · Pocket 19
P2Rank 0.674 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 537 / 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.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • 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:0000287 Binding to a magnesium (Mg) ion.
  • 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: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:0004450 Catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH.
  • GO:0006097 A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
29 412 Pfam PF00180 Isocitrate/isopropylmalate dehydrogenase
29 412 InterPro IPR024084 Isopropylmalate dehydrogenase-like domain
1 416 NCBIfam TIGR00183 isocitrate dehydrogenase (NADP(+))
1 416 InterPro IPR004439 Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic
3 416 SUPERFAMILY SSF53659 Isocitrate/Isopropylmalate dehydrogenase-like
303 322 ProSitePatterns PS00470 Isocitrate and isopropylmalate dehydrogenases signature.
303 322 InterPro IPR019818 Isocitrate/isopropylmalate dehydrogenase, conserved site
28 412 SMART SM01329 Iso_dh_2
28 412 InterPro IPR024084 Isopropylmalate dehydrogenase-like domain
1 416 PANTHER PTHR43504 ISOCITRATE DEHYDROGENASE [NADP]
1 416 FunFam G3DSA:3.40.718.10:FF:000005 Isocitrate dehydrogenase [NADP]
1 416 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_A0A0H3GVN3
AlphaFold — — full sequence — Viewing
ColabFold KP13_04861
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
1 0.449

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 11.91 0.631
2 4.01 0.16
3 1.82 0.035

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.

61 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
A2P
4AJS
P08200 427.2 Da LogP -1.75 TPSA 232.6 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AKG
1BL5
P08200 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
EE1
6C0E
Q5ZXB6 889.5 Da LogP -3.60 TPSA 455.8 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ENP
1TYO
Q9YE81 663.3 Da LogP -2.50 TPSA 316.4 3 viol. ✓ Clean c1cn2cnc3c(c2n1)ncn3[C@H]4[C@@H]([C@@H]([C@H](O…
FLC
2D4V
Q8GAX0 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
ICA
1AI2
P08200 231.2 Da LogP -1.28 TPSA 121.1 ✓ Ro5 ✓ Clean C([C@@H]([C@H](C(=O)O)O[Ca])C(=O)O)C(=O)O
ICT
1CW1
P08200 192.1 Da LogP -1.39 TPSA 132.1 ✓ Ro5 ✓ Clean C([C@@H]([C@H](C(=O)O)O)C(=O)O)C(=O)O
NDO
1AI3
P08200 744.4 Da LogP -3.41 TPSA 361.8 3 viol. ✓ Clean c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P…
NMN
4AJR
P08200 335.2 Da LogP -2.20 TPSA 163.4 ✓ Ro5 ✓ Clean c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(…
OXS
1IDC
P08200 190.1 Da LogP -1.18 TPSA 129.0 ✓ Ro5 ✓ Clean C([C@@H](C(=O)C(=O)O)C(=O)O)C(=O)O
TAP
4AJA
P08200 759.5 Da LogP -3.00 TPSA 350.6 3 viol. ✓ Clean c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P…

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.