Protein profile

PA2623

isocitrate dehydrogenase

Genome: NC_002516.2

Gene: icd PA2623 Structure source: AlphaFold UniProt Q9I0L5

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Amino acids 418

Annotations 7

Features 12

PDB binders 11

Druggability 0.873

Overview

Basic information about this protein and its source genome.

Accession: PA2623
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: icd PA2623
Status: annotated
Amino acids: 418
Structure source: AlphaFold

1.1.1.42

GO:0004450 Catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH. 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: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. 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: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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 45.161
Human E-value: 2.05e-07
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

Selected Druggability evidence

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 0.873

Structure –

Pocket –

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)

1.1.1.42

Gene Ontology (GO)

GO:0004450 Catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH.
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: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.
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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
3	418	NCBIfam	TIGR00183	isocitrate dehydrogenase (NADP(+))
3	418	InterPro	IPR004439	Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic
305	324	ProSitePatterns	PS00470	Isocitrate and isopropylmalate dehydrogenases signature.
305	324	InterPro	IPR019818	Isocitrate/isopropylmalate dehydrogenase, conserved site
30	414	SMART	SM01329	Iso_dh_2
30	414	InterPro	IPR024084	Isopropylmalate dehydrogenase-like domain
31	413	Pfam	PF00180	Isocitrate/isopropylmalate dehydrogenase
31	413	InterPro	IPR024084	Isopropylmalate dehydrogenase-like domain
2	418	FunFam	G3DSA:3.40.718.10:FF:000005	Isocitrate dehydrogenase [NADP]
1	418	Gene3D	G3DSA:3.40.718.10	Isopropylmalate Dehydrogenase
4	418	SUPERFAMILY	SSF53659	Isocitrate/Isopropylmalate dehydrogenase-like
3	418	PANTHER	PTHR43504	ISOCITRATE DEHYDROGENASE [NADP]

3D Structure

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

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA2623	AlphaFold	—	—	full sequence	—	Viewing

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				0.873
4				0.377

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

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
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…`

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).

No ChEMBL hits found through similar proteins.

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
ZINC12503278	1.000	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…`
ZINC1532667	1.000	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@H]2O[C@@H](COP(=O)(O)O)[C@H]…`
ZINC2545161	1.000	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@@H](COP(=O)(O)O)[C@H…`
ZINC3870109	1.000	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@@H](COP(=O)(O)O)[C@@…`
ZINC3871404	1.000	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC40465856	1.000	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…`
ZINC40762833	1.000	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@H]2O[C@H](COP(=O)(O)O)[C@@H]…`
ZINC4228273	1.000	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…`
ZINC77311638	1.000	335.2 Da LogP -2.20 TPSA 163.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…`
ZINC4095572	0.809	336.2 Da LogP -1.60 TPSA 157.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…`
ZINC77311659	0.809	336.2 Da LogP -1.60 TPSA 157.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…`
ZINC77311660	0.809	336.2 Da LogP -1.60 TPSA 157.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@H]…`
ZINC77311661	0.809	336.2 Da LogP -1.60 TPSA 157.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc[n+]([C@@H]2O[C@H](COP(=O)(O)O)[C@@H…`
ZINC13507175	0.766	451.2 Da LogP -1.08 TPSA 211.0	1 viol.	✓ Clean	`O=P(O)(O)O[P@](=O)(O)OC[C@H]1O[C@@H](n2cnc3c2nc…`
ZINC25756940	0.760	331.3 Da LogP 0.35 TPSA 123.0	✓ Ro5	✓ Clean	`C[C@@H]1[C@@H](COP(=O)(O)O)O[C@@H]([n+]2cccc(C(…`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC1776011316	0.700	333.3 Da LogP -1.74 TPSA 154.2	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CCP(=O)(O)O)[C@@H…`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC1577651	0.684	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O`
ZINC1577652	0.684	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O`
ZINC1577653	0.684	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](C(=O)O)[C@H](CC(=O)O)C(=O)O`
ZINC14613564	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO)[C@@H](O)[C@@H…`
ZINC34633968	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@H]2O[C@H](CO)[C@@H](O)[C@H]2…`
ZINC4096036	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]…`
ZINC65748069	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO)[C@H](O)[C@H]2…`
ZINC65748073	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@@H]2O[C@H](CO)[C@H](O)[C@@H]…`
ZINC901659	0.681	255.2 Da LogP -2.32 TPSA 116.9	✓ Ro5	✓ Clean	`NC(=O)c1ccc[n+]([C@H]2O[C@@H](CO)[C@H](O)[C@@H]…`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC14686440	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC5811921	0.604	333.2 Da LogP -0.94 TPSA 159.5	✓ Ro5	✓ Clean	`NC(=O)c1cccc([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC5811924	0.604	333.2 Da LogP -0.94 TPSA 159.5	✓ Ro5	✓ Clean	`NC(=O)c1cccc([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC5811925	0.604	333.2 Da LogP -0.94 TPSA 159.5	✓ Ro5	✓ Clean	`NC(=O)c1cccc([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC5811926	0.604	333.2 Da LogP -0.94 TPSA 159.5	✓ Ro5	✓ Clean	`NC(=O)c1cccc([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC25762090	0.580	355.2 Da LogP -0.16 TPSA 144.2	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](n2cnc3c2ncn2ccnc32)C[C…`
ZINC13398039	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC2528012	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315135	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315336	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@](O)(CC(=O)O)C(=O)O`
ZINC3871401	0.556	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3871402	0.556	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3871403	0.556	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC4096223	0.556	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC1601494	0.554	291.3 Da LogP -1.31 TPSA 117.9	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@@H](n2cnc3c2ncn2ccnc32)[C@H](O)[C@…`
ZINC3814308	0.554	291.3 Da LogP -1.31 TPSA 117.9	✓ Ro5	✓ Clean	`OC[C@H]1O[C@@H](n2cnc3c2ncn2ccnc32)[C@H](O)[C@@…`
ZINC3872479	0.554	291.3 Da LogP -1.31 TPSA 117.9	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@H](n2cnc3c2ncn2ccnc32)[C@H](O)[C@@…`
ZINC3872481	0.554	291.3 Da LogP -1.31 TPSA 117.9	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@H](n2cnc3c2ncn2ccnc32)[C@@H](O)[C@…`
ZINC3872482	0.554	291.3 Da LogP -1.31 TPSA 117.9	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@@H](n2cnc3c2ncn2ccnc32)[C@@H](O)[C…`

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.