Amino acids
910
Annotations
15
Features
46
PDB binders
11
Druggability
0.524
Overview
Basic information about this protein and its source genome.
- Accession
- PA1562
- Gene
- acnA PA1562
- Status
- annotated
- Amino acids
- 910
- Structure source
- AlphaFold
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0047456 Catalysis of the reaction: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = cis-2-methylaconitate + H2O.
GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
GO:0003994 Catalysis of the reaction: citrate = isocitrate. The reaction occurs in two steps: (1) citrate = cis-aconitate + H2O, (2) cis-aconitate + H2O = isocitrate. This reaction is the interconversion of citrate and isocitrate via the labile, enzyme-bound intermediate cis-aconitate. Water is removed from one part of the citrate molecule and added back to a different atom to form isocitrate.
GO:0005506 Binding to an iron (Fe) ion.
Target profile
Computed evidence for target prioritization.
- Human off-target
- hit
- Human identity (%)
- 53.348
- Human E-value
- 0.0
- 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
0.524
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
2 EC
13 GO
Gene Ontology (GO)
13- GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
- GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
- GO:0047456 Catalysis of the reaction: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = cis-2-methylaconitate + H2O.
- GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
- GO:0003994 Catalysis of the reaction: citrate = isocitrate. The reaction occurs in two steps: (1) citrate = cis-aconitate + H2O, (2) cis-aconitate + H2O = isocitrate. This reaction is the interconversion of citrate and isocitrate via the labile, enzyme-bound intermediate cis-aconitate. Water is removed from one part of the citrate molecule and added back to a different atom to form isocitrate.
- GO:0005506 Binding to an iron (Fe) ion.
- GO:0030350 Binding to an iron-responsive element, a regulatory sequence found in the 5'- and 3'-untranslated regions of mRNAs encoding many iron-binding proteins.
- GO:0003730 Binding to a 3' untranslated region of an mRNA molecule.
- GO:0003729 Binding to messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
- GO:0009061 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
- GO:0019679 OBSOLETE. The chemical reactions and pathways involving propionate that occur in the methylcitrate cycle.
- GO:0006979 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
- 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.
Sequence Features
Domain/signature hits from InterPro and related databases.
46 records
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 649 | 909 | SUPERFAMILY | SSF52016 | LeuD/IlvD-like |
| 673 | 910 | Gene3D | G3DSA:3.20.19.10 | Aconitase, domain 4 |
| 673 | 910 | InterPro | IPR015928 | Aconitase/3-isopropylmalate dehydratase, swivel |
| 18 | 910 | NCBIfam | TIGR01341 | aconitate hydratase AcnA |
| 18 | 910 | InterPro | IPR006249 | Aconitase/Iron-responsive element-binding protein 2 |
| 450 | 461 | PRINTS | PR00415 | Aconitase family signature |
| 450 | 461 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 372 | 386 | PRINTS | PR00415 | Aconitase family signature |
| 372 | 386 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 279 | 292 | PRINTS | PR00415 | Aconitase family signature |
| 279 | 292 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 170 | 178 | PRINTS | PR00415 | Aconitase family signature |
| 170 | 178 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 293 | 306 | PRINTS | PR00415 | Aconitase family signature |
| 293 | 306 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 512 | 525 | PRINTS | PR00415 | Aconitase family signature |
| 512 | 525 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 203 | 216 | PRINTS | PR00415 | Aconitase family signature |
| 203 | 216 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 146 | 159 | PRINTS | PR00415 | Aconitase family signature |
| 146 | 159 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 217 | 232 | PRINTS | PR00415 | Aconitase family signature |
| 217 | 232 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 610 | 669 | Gene3D | G3DSA:6.10.190.10 | - |
| 373 | 609 | FunFam | G3DSA:3.30.499.10:FF:000009 | Aconitate hydratase |
| 85 | 583 | CDD | cd01586 | AcnA_IRP |
| 373 | 609 | Gene3D | G3DSA:3.30.499.10 | Aconitase, domain 3 |
| 373 | 609 | InterPro | IPR015931 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 |
| 686 | 856 | CDD | cd01580 | AcnA_IRP_Swivel |
| 686 | 856 | InterPro | IPR044137 | Aconitase A, swivel domain |
| 74 | 581 | Pfam | PF00330 | Aconitase family (aconitate hydratase) |
| 74 | 581 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 672 | 910 | FunFam | G3DSA:3.20.19.10:FF:000001 | Aconitate hydratase |
| 5 | 645 | SUPERFAMILY | SSF53732 | Aconitase iron-sulfur domain |
| 5 | 645 | InterPro | IPR036008 | Aconitase, iron-sulfur domain |
| 14 | 909 | PANTHER | PTHR11670 | ACONITASE/IRON-RESPONSIVE ELEMENT FAMILY MEMBER |
| 14 | 909 | InterPro | IPR006249 | Aconitase/Iron-responsive element-binding protein 2 |
| 5 | 372 | FunFam | G3DSA:3.30.499.10:FF:000002 | Aconitate hydratase |
| 710 | 837 | Pfam | PF00694 | Aconitase C-terminal domain |
| 710 | 837 | InterPro | IPR000573 | Aconitase A/isopropylmalate dehydratase small subunit, swivel domain |
| 6 | 372 | Gene3D | G3DSA:3.30.499.10 | Aconitase, domain 3 |
| 6 | 372 | InterPro | IPR015931 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 |
| 512 | 525 | ProSitePatterns | PS01244 | Aconitase family signature 2. |
| 512 | 525 | InterPro | IPR018136 | Aconitase family, 4Fe-4S cluster binding site |
| 446 | 462 | ProSitePatterns | PS00450 | Aconitase family signature 1. |
| 446 | 462 | InterPro | IPR018136 | Aconitase family, 4Fe-4S cluster binding site |
3D Structure
Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.
Loading 3D structure...
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Structural evidence
0 + 1Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
PA1562
|
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 |
|---|---|---|---|---|---|---|---|
| 2 | 0.524 |
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.
25 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 |
|---|---|---|---|---|---|---|
| ATH | P20004 | 187.1 Da LogP -5.48 TPSA 140.6 | ✓ Ro5 | ✓ Clean |
C(=C(/[C@H](C(=O)[O-])O)\C(=O)[O-])/C(=O)[O-]
|
|
| F3S | P16276 | 295.8 Da LogP 2.59 TPSA 0.0 | ✓ Ro5 | ✓ Clean |
S1[Fe]2S[Fe]3[S]2[Fe]1S3
|
|
| FLC | P16276 | 189.1 Da LogP -5.25 TPSA 140.6 | ✓ Ro5 | ✓ Clean |
C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
|
|
| ICT | P16276 | 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
|
|
| KP1 | P81291 | 132.2 Da LogP 0.92 TPSA 40.5 | ✓ Ro5 | ✓ Clean |
CC(C)(CC(C)(C)O)O
|
|
| MIC | P20004 | 206.2 Da LogP -1.00 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
C[C@@]([C@H](CC(=O)O)C(=O)O)(C(=O)O)O
|
|
| NIC | P20004 | 193.1 Da LogP -1.45 TPSA 138.0 | ✓ Ro5 | ✓ Clean |
C([C@@H]([C@H](C(=O)O)O)[N+](=O)[O-])C(=O)O
|
|
| NTC | P20004 | 193.1 Da LogP -1.45 TPSA 138.0 | ✓ Ro5 | ✓ Clean |
C(C(=O)O)[C@@](C[N+](=O)[O-])(C(=O)O)O
|
|
| O | P16276 | 18.0 Da LogP -0.82 TPSA 31.5 | ✓ Ro5 | ✓ Clean |
O
|
|
| TRA | P20004 | 171.1 Da LogP -4.45 TPSA 120.4 | ✓ Ro5 | ✓ Clean |
C(/C(=C\C(=O)[O-])/C(=O)[O-])C(=O)[O-]
|
|
| TRC | P16276 | 176.1 Da LogP -0.36 TPSA 111.9 | ✓ Ro5 | ✓ Clean |
C(C(CC(=O)O)C(=O)O)C(=O)O
|
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 |
|---|---|---|---|---|---|
| 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
|
| ZINC1623550 | 0.529 | 240.1 Da LogP 2.00 TPSA 40.5 | ✓ Ro5 | ✓ Clean |
CC(C)(O)CC(O)(C(F)(F)F)C(F)(F)F
|
| ZINC45068939 | 0.519 | 252.2 Da LogP 1.14 TPSA 111.9 | ✓ Ro5 | ✓ Clean |
O=C(O)C[C@H](CC(=O)c1ccc(O)cc1)C(=O)O
|
| ZINC45068942 | 0.519 | 252.2 Da LogP 1.14 TPSA 111.9 | ✓ Ro5 | ✓ Clean |
O=C(O)C[C@@H](CC(=O)c1ccc(O)cc1)C(=O)O
|
| ZINC168333116 | 0.515 | 225.2 Da LogP 0.32 TPSA 100.7 | ✓ Ro5 | ✓ Clean |
O=C(O)[C@@H](O)[C@H](Cc1ccccc1)[N+](=O)[O-]
|
| ZINC168342027 | 0.515 | 225.2 Da LogP 0.32 TPSA 100.7 | ✓ Ro5 | ✓ Clean |
O=C(O)[C@H](O)[C@H](Cc1ccccc1)[N+](=O)[O-]
|
| ZINC33992595 | 0.515 | 225.2 Da LogP 0.32 TPSA 100.7 | ✓ Ro5 | ✓ Clean |
O=C(O)[C@@H](O)[C@@H](Cc1ccccc1)[N+](=O)[O-]
|
| ZINC34050089 | 0.515 | 225.2 Da LogP 0.32 TPSA 100.7 | ✓ Ro5 | ✓ Clean |
O=C(O)[C@H](O)[C@@H](Cc1ccccc1)[N+](=O)[O-]
|
| ZINC1532902 | 0.500 | 206.2 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC2018106 | 0.500 | 206.2 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC[C@](O)(CC(=O)O)C(=O)O
|
| ZINC4212247 | 0.500 | 292.1 Da LogP -1.16 TPSA 189.7 | 1 viol. | ✓ Clean |
O=C(O)C[C@@H](C(=O)O)C(P(=O)(O)O)P(=O)(O)O
|
| ZINC5131772 | 0.500 | 292.1 Da LogP -1.16 TPSA 189.7 | 1 viol. | ✓ Clean |
O=C(O)C[C@H](C(=O)O)C(P(=O)(O)O)P(=O)(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.