Overview
Basic information about this protein and its source genome.
- Accession
- VK055_2445
- Gene
- acnB AIK81042.1
- Status
- annotated
- Amino acids
- 839
- Structure source
- AlphaFold + ColabFold
Target profile
Computed evidence for target prioritization.
- Human off-target
- No hit
- Human identity (%)
- 0.0
- Gut microbiome off-target
- hit
- Essential (DEG)
- Y
- DEG identity (%)
- 96.782
- DEG E-value
- 0.0
- Localization
- Cytoplasmic
- ColabFold pLDDT
- 97.56
Selected Druggability evidence
AlphaFold / UniProt modelSelected 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.
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Gene Ontology (GO)
8- 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: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: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:0046872 Binding to a metal ion.
- GO:0003730 Binding to a 3' untranslated region of an mRNA molecule.
- GO:0019629 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of propionate that occurs in the 2-methylcitrate cycle.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 358 | 794 | CDD | cd01581 | AcnB |
| 676 | 693 | ProSitePatterns | PS00450 | Aconitase family signature 1. |
| 676 | 693 | InterPro | IPR018136 | Aconitase family, 4Fe-4S cluster binding site |
| 356 | 655 | Gene3D | G3DSA:3.40.1060.10 | Aconitase, Domain 2 |
| 356 | 655 | InterPro | IPR015932 | Aconitase, domain 2 |
| 145 | 285 | CDD | cd01576 | AcnB_Swivel |
| 145 | 285 | InterPro | IPR015929 | Aconitase B, swivel |
| 1 | 135 | Gene3D | G3DSA:1.25.40.310 | - |
| 1 | 135 | InterPro | IPR036288 | Aconitase B, HEAT-like domain superfamily |
| 376 | 503 | FunFam | G3DSA:3.30.499.10:FF:000001 | Aconitate hydratase B |
| 136 | 345 | SUPERFAMILY | SSF52016 | LeuD/IlvD-like |
| 657 | 839 | FunFam | G3DSA:3.30.499.10:FF:000008 | Aconitate hydratase B |
| 353 | 833 | SUPERFAMILY | SSF53732 | Aconitase iron-sulfur domain |
| 353 | 833 | InterPro | IPR036008 | Aconitase, iron-sulfur domain |
| 657 | 839 | Gene3D | G3DSA:3.30.499.10 | Aconitase, domain 3 |
| 657 | 839 | InterPro | IPR015931 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 |
| 2 | 130 | Pfam | PF11791 | Aconitate B N-terminal domain |
| 2 | 130 | InterPro | IPR015933 | Aconitase B, HEAT-like domain |
| 2 | 134 | SUPERFAMILY | SSF74778 | Aconitase B, N-terminal domain |
| 2 | 134 | InterPro | IPR036288 | Aconitase B, HEAT-like domain superfamily |
| 446 | 792 | Pfam | PF00330 | Aconitase family (aconitate hydratase) |
| 446 | 792 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 136 | 335 | FunFam | G3DSA:3.20.19.10:FF:000004 | Aconitate hydratase B |
| 488 | 655 | FunFam | G3DSA:3.40.1060.10:FF:000002 | Aconitate hydratase B |
| 376 | 503 | Gene3D | G3DSA:3.30.499.10 | Aconitase, domain 3 |
| 376 | 503 | InterPro | IPR015931 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 |
| 136 | 335 | Gene3D | G3DSA:3.20.19.10 | Aconitase, domain 4 |
| 136 | 335 | InterPro | IPR015928 | Aconitase/3-isopropylmalate dehydratase, swivel |
| 735 | 748 | ProSitePatterns | PS01244 | Aconitase family signature 2. |
| 735 | 748 | InterPro | IPR018136 | Aconitase family, 4Fe-4S cluster binding site |
| 1 | 833 | PIRSF | PIRSF036687 | AcnB |
| 1 | 833 | InterPro | IPR004406 | Aconitase B |
| 1 | 135 | FunFam | G3DSA:1.25.40.310:FF:000001 | Aconitate hydratase B |
| 142 | 356 | Pfam | PF06434 | Aconitate hydratase 2 N-terminus |
| 142 | 356 | InterPro | IPR015929 | Aconitase B, swivel |
| 1 | 828 | NCBIfam | TIGR00117 | bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase |
| 1 | 828 | InterPro | IPR004406 | Aconitase B |
| 219 | 800 | PANTHER | PTHR43160 | ACONITATE HYDRATASE B |
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...
Structural evidence
0 + 2Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
AF_A0A0H3GJE4
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_2445
|
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 |
|---|---|---|---|---|---|---|---|
| 16 | 0.217 |
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 | 18.0 | 0.813 | ||||||
| 2 | 7.15 | 0.371 | ||||||
| 3 | 7.0 | 0.362 | ||||||
| 4 | 5.72 | 0.277 | ||||||
| 5 | 2.72 | 0.081 |
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 | 0.332 | ||||||
| 20 | 0.221 |
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 | 16.07 | 0.769 | ||||||
| 2 | 6.67 | 0.339 | ||||||
| 3 | 6.19 | 0.309 | ||||||
| 4 | 4.98 | 0.225 | ||||||
| 5 | 3.17 | 0.108 |
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.
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 | P36683 | 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 | P36683 | 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.