Protein profile
KP13_01971
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Genome: KpKP13
Overview
Basic information about this protein and its source genome.
- Accession
- KP13_01971
- Gene
- ispH AHE46410.1
- Status
- annotated
- Amino acids
- 316
- 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 (%)
- 93.671
- DEG E-value
- 0.0
- Localization
- Cytoplasmic
- ColabFold pLDDT
- 97.25
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)
7- GO:0050992 The chemical reactions and pathways resulting in the formation of dimethylallyl diphosphate.
- GO:0046872 Binding to a metal ion.
- GO:0019288 The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
- GO:0051745 Catalyzes the conversion of (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H+ + 2 reduced [2Fe-2S]-[ferredoxin] to isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) releasing H2O + 2 oxidized [2Fe-2S]-[ferredoxin]. Note that (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate is an alternative name for 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate.
- GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
- 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:0016114 The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 12 | 96 | FunFam | G3DSA:3.40.50.11270:FF:000001 | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase |
| 1 | 286 | Hamap | MF_00191 | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase [ispH]. |
| 1 | 286 | InterPro | IPR003451 | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase |
| 97 | 196 | Gene3D | G3DSA:3.40.1010.20 | - |
| 2 | 284 | NCBIfam | TIGR00216 | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase |
| 2 | 284 | InterPro | IPR003451 | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase |
| 3 | 282 | CDD | cd13944 | lytB_ispH |
| 3 | 282 | InterPro | IPR003451 | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase |
| 1 | 314 | PANTHER | PTHR30426 | 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE |
| 1 | 314 | InterPro | IPR003451 | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase |
| 3 | 282 | Pfam | PF02401 | LytB protein |
| 12 | 96 | Gene3D | G3DSA:3.40.50.11270 | - |
| 5 | 281 | Gene3D | G3DSA:3.40.1010.20 | - |
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_A0A0H3GN13
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
KP13_01971
|
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 |
|---|---|---|---|---|---|---|---|
| 2 | 0.749 |
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 | 14.84 | 0.736 |
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 |
|---|---|---|---|---|---|---|---|
| 3 | 0.724 | ||||||
| 1 | 0.476 |
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 | 16.23 | 0.774 |
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 |
|---|---|---|---|---|---|---|
| 0CG | P62623 | 216.0 Da LogP -0.15 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
C#CCOP(=O)(O)OP(=O)(O)O
|
|
| 0CH | P62623 | 250.1 Da LogP -0.01 TPSA 133.5 | ✓ Ro5 | ✓ Clean |
C(CCOP(=O)(O)OP(=O)(O)O)CO
|
|
| 0CJ | P62623 | 262.1 Da LogP 0.58 TPSA 130.4 | ✓ Ro5 | ✓ Clean |
CC(=O)CCCOP(=O)(O)OP(=O)(O)O
|
|
| 0CM | P62623 | 230.0 Da LogP 0.24 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
CC#CCOP(=O)(O)OP(=O)(O)O
|
|
| 0CN | P62623 | 230.0 Da LogP 0.55 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
C=C=CCOP(=O)(O)OP(=O)(O)O
|
|
| 0JX | P62623 | 248.1 Da LogP 0.67 TPSA 133.5 | ✓ Ro5 | ✓ Clean |
C(COP(=O)(O)OP(=O)(O)O)/C=C/O
|
|
| 0K2 | P62623 | 248.1 Da LogP 0.19 TPSA 130.4 | ✓ Ro5 | ✓ Clean |
C(CC=O)COP(=O)(O)OP(=O)(O)O
|
|
| 0O3 | P62623 | 262.1 Da LogP 0.15 TPSA 133.5 | ✓ Ro5 | ✓ Clean |
C=C(CCOP(=O)(O)OP(=O)(O)O)CO
|
|
| 10D | P62623 | 264.1 Da LogP 1.13 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
C/C(=C\COP(=O)(O)OP(=O)(O)O)/CF
|
|
| 10E | P62623 | 261.1 Da LogP 0.12 TPSA 139.3 | ✓ Ro5 | ✓ Clean |
C/C(=C\COP(=O)(O)OP(=O)(O)O)/CN
|
|
| 10G | P62623 | 278.2 Da LogP 1.09 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
C/C(=C\COP(=O)(O)OP(=O)(O)O)/CS
|
|
| DMA | P62623 | 246.1 Da LogP 1.18 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
CC(=CCO[P@@](=O)(O)OP(=O)(O)O)C
|
|
| EIP | P62623 | 264.1 Da LogP 0.23 TPSA 133.5 | ✓ Ro5 | ✓ Clean |
C[C@@H](CCO[P@](=O)(O)OP(=O)(O)O)CO
|
|
| F3S | P62623 | 295.8 Da LogP 2.59 TPSA 0.0 | ✓ Ro5 | ✓ Clean |
S1[Fe]2S[Fe]3[S]2[Fe]1S3
|
|
| H6P | P62623 | 262.1 Da LogP 0.15 TPSA 133.5 | ✓ Ro5 | ✓ Clean |
C/C(=C\CO[P@@](=O)(O)OP(=O)(O)O)/CO
|
|
| IPE | P62623 | 246.1 Da LogP 1.18 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
CC(=C)CCO[P@@](=O)(O)OP(=O)(O)O
|
|
| POP | P62623 | 176.0 Da LogP -2.08 TPSA 129.9 | ✓ Ro5 | ✓ Clean |
O[P@@](=O)([O-])O[P@@](=O)(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).
| Ligand | UniProt (homolog) | pchembl | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| 43W | O67625 | 7.22 | 230.0 Da LogP 0.24 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
C#CCCOP(=O)(O)OP(=O)(O)O
|
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 |
|---|---|---|---|---|---|
| ZINC8215654 | 1.000 | 246.1 Da LogP 1.18 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
C=C(C)CCO[P@@](=O)(O)OP(=O)(O)O
|
| ZINC8215740 | 1.000 | 246.1 Da LogP 1.18 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
CC(C)=CCO[P@@](=O)(O)OP(=O)(O)O
|
| ZINC8436838 | 1.000 | 262.1 Da LogP 0.15 TPSA 133.5 | ✓ Ro5 | ✓ Clean |
C/C(=C\CO[P@@](=O)(O)OP(=O)(O)O)CO
|
| ZINC71769106 | 0.923 | 326.1 Da LogP 1.30 TPSA 159.8 | ✓ Ro5 | ✓ Clean |
CC(C)=CCO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O
|
| ZINC8215849 | 0.719 | 314.2 Da LogP 2.91 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
CC(C)=CCC/C(C)=C/CO[P@@](=O)(O)OP(=O)(O)O
|
| ZINC2579357 | 0.700 | 248.1 Da LogP 1.26 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
CC(C)CCO[P@](=O)(O)OP(=O)(O)O
|
| ZINC12494625 | 0.697 | 382.3 Da LogP 4.63 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
CC(C)=CCC/C(C)=C/CC/C(C)=C/CO[P@@](=O)(O)OP(=O)…
|
| ZINC2356589248 | 0.697 | 382.3 Da LogP 4.63 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
CC(C)=CCCC(C)=CCCC(C)=CCO[P@](=O)(O)OP(=O)(O)O
|
| ZINC34661063 | 0.676 | 394.2 Da LogP 3.02 TPSA 159.8 | ✓ Ro5 | ✓ Clean |
CC(C)=CCC/C(C)=C/CO[P@@](=O)(O)O[P@@](=O)(O)OP(…
|
| ZINC8218174 | 0.657 | 462.3 Da LogP 4.75 TPSA 159.8 | ✓ Ro5 | ✓ Clean |
CC(C)=CCC/C(C)=C/CC/C(C)=C/CO[P@@](=O)(O)O[P@@]…
|
| ZINC34020319 | 0.588 | 260.1 Da LogP 0.61 TPSA 124.3 | ✓ Ro5 | ✓ Clean |
C/C(=C\CC[P@@](=O)(O)OP(=O)(O)O)CO
|
| ZINC13539354 | 0.571 | 332.2 Da LogP 3.20 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
CC(C)=CCC/C(C)=C(\F)CO[P@](=O)(O)OP(=O)(O)O
|
| ZINC39419974 | 0.520 | 212.1 Da LogP 1.04 TPSA 44.8 | ✓ Ro5 | ✓ Clean |
C#CCOP(=O)(OCC#C)OCC#C
|
| ZINC1532829 | 0.500 | 234.2 Da LogP 2.79 TPSA 66.8 | ✓ Ro5 | ✓ Clean |
CC(C)=CCC/C(C)=C/COP(=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.