Protein profile
KP13_01923
3-isopropylmalate dehydratase large subunit
Genome: KpKP13
Overview
Basic information about this protein and its source genome.
- Accession
- KP13_01923
- Gene
- AHE46364.1 leuC
- Status
- annotated
- Amino acids
- 466
- Structure source
- AlphaFold + ColabFold
Target profile
Computed evidence for target prioritization.
- Human off-target
- hit
- Human identity (%)
- 26.768
- Human E-value
- 2.05e-23
- Gut microbiome off-target
- hit
- Essential (DEG)
- Y
- DEG identity (%)
- 76.18
- DEG E-value
- 0.0
- Localization
- Cytoplasmic
- ColabFold pLDDT
- 97.31
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.
Enzyme Commission (EC)
1Gene Ontology (GO)
5- GO:0003861 Catalysis of the reaction: (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate.
- 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:0009098 The chemical reactions and pathways resulting in the formation of L-leucine, 2-amino-4-methylpentanoic acid.
- GO:0016853 Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
- GO:0046872 Binding to a metal ion.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 29 | 459 | CDD | cd01583 | IPMI |
| 29 | 459 | InterPro | IPR033941 | 3-Isopropylmalate dehydratase, catalytic domain |
| 2 | 465 | SUPERFAMILY | SSF53732 | Aconitase iron-sulfur domain |
| 2 | 465 | InterPro | IPR036008 | Aconitase, iron-sulfur domain |
| 286 | 300 | PRINTS | PR00415 | Aconitase family signature |
| 286 | 300 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 82 | 95 | PRINTS | PR00415 | Aconitase family signature |
| 82 | 95 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 119 | 132 | PRINTS | PR00415 | Aconitase family signature |
| 119 | 132 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 195 | 208 | PRINTS | PR00415 | Aconitase family signature |
| 195 | 208 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 343 | 354 | PRINTS | PR00415 | Aconitase family signature |
| 343 | 354 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 399 | 412 | PRINTS | PR00415 | Aconitase family signature |
| 399 | 412 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 209 | 222 | PRINTS | PR00415 | Aconitase family signature |
| 209 | 222 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 133 | 148 | PRINTS | PR00415 | Aconitase family signature |
| 133 | 148 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 108 | 116 | PRINTS | PR00415 | Aconitase family signature |
| 108 | 116 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 7 | 457 | Pfam | PF00330 | Aconitase family (aconitate hydratase) |
| 7 | 457 | InterPro | IPR001030 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain |
| 2 | 465 | PANTHER | PTHR43822 | HOMOACONITASE, MITOCHONDRIAL-RELATED |
| 399 | 412 | ProSitePatterns | PS01244 | Aconitase family signature 2. |
| 399 | 412 | InterPro | IPR018136 | Aconitase family, 4Fe-4S cluster binding site |
| 4 | 286 | Gene3D | G3DSA:3.30.499.10 | Aconitase, domain 3 |
| 4 | 286 | InterPro | IPR015931 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 |
| 4 | 286 | FunFam | G3DSA:3.30.499.10:FF:000006 | 3-isopropylmalate dehydratase large subunit |
| 339 | 355 | ProSitePatterns | PS00450 | Aconitase family signature 1. |
| 339 | 355 | InterPro | IPR018136 | Aconitase family, 4Fe-4S cluster binding site |
| 1 | 465 | NCBIfam | TIGR00170 | 3-isopropylmalate dehydratase large subunit |
| 1 | 465 | InterPro | IPR004430 | 3-isopropylmalate dehydratase, large subunit |
| 327 | 466 | Gene3D | G3DSA:3.30.499.10 | Aconitase, domain 3 |
| 327 | 466 | InterPro | IPR015931 | Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 |
| 327 | 466 | FunFam | G3DSA:3.30.499.10:FF:000007 | 3-isopropylmalate dehydratase large subunit |
| 1 | 466 | Hamap | MF_01026 | 3-isopropylmalate dehydratase large subunit [leuC]. |
| 1 | 466 | InterPro | IPR004430 | 3-isopropylmalate dehydratase, large subunit |
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_A0A0H3GMJ2
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
KP13_01923
|
ColabFold | — | — | full sequence | — | Loaded |
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer
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 | 6.98 | 0.361 | ||||||
| 2 | 2.38 | 0.063 | ||||||
| 3 | 1.97 | 0.041 | ||||||
| 4 | 1.95 | 0.041 |
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 |
|---|---|---|---|---|---|---|---|
| 17 | 0.644 |
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 | 7.5 | 0.395 | ||||||
| 2 | 3.87 | 0.151 | ||||||
| 3 | 2.17 | 0.052 | ||||||
| 4 | 2.03 | 0.044 | ||||||
| 5 | 1.57 | 0.024 |
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 | 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.