Protein profile
VK055_4655
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
Genome: KpATCC43816
Overview
Basic information about this protein and its source genome.
- Accession
- VK055_4655
- Gene
- AIK83189.1 ispG
- Status
- annotated
- Amino acids
- 373
- 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 (%)
- 99.191
- DEG E-value
- 0.0
- Localization
- Cytoplasmic
- ColabFold pLDDT
- 93.89
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)
5- GO:0046429 Catalysis of the reaction: (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate + H2O + 2 oxidized ferredoxin = 2-C-methyl-D-erythritol 2,4-cyclodiphosphate + 2 reduced ferredoxin.
- 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.
- GO:0005506 Binding to an iron (Fe) ion.
- GO:0044237 OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances.
- GO:0008299 The chemical reactions and pathways resulting in the formation of an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 1 | 261 | Gene3D | G3DSA:3.20.20.20 | - |
| 1 | 261 | InterPro | IPR011005 | Dihydropteroate synthase-like |
| 262 | 361 | FunFam | G3DSA:3.30.413.10:FF:000002 | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) |
| 1 | 261 | FunFam | G3DSA:3.20.20.20:FF:000001 | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) |
| 265 | 352 | SUPERFAMILY | SSF56014 | Nitrite and sulphite reductase 4Fe-4S domain-like |
| 265 | 352 | InterPro | IPR045854 | Nitrite and sulphite reductase 4Fe-4S domain-like superfamily |
| 345 | 365 | Coils | Coil | Coil |
| 7 | 357 | Hamap | MF_00159 | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (ferredoxin) [ispG]. |
| 7 | 357 | InterPro | IPR004588 | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial-type |
| 1 | 363 | PIRSF | PIRSF004640 | IspG |
| 1 | 363 | InterPro | IPR016425 | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial |
| 13 | 353 | Pfam | PF04551 | GcpE protein |
| 13 | 353 | InterPro | IPR004588 | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial-type |
| 262 | 360 | Gene3D | G3DSA:3.30.413.10 | Sulfite Reductase Hemoprotein, domain 1 |
| 262 | 360 | InterPro | IPR045854 | Nitrite and sulphite reductase 4Fe-4S domain-like superfamily |
| 9 | 350 | NCBIfam | TIGR00612 | (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase |
| 9 | 350 | InterPro | IPR004588 | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial-type |
| 250 | 360 | PANTHER | PTHR30454 | 4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASE |
| 250 | 360 | InterPro | IPR004588 | 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase, bacterial-type |
| 15 | 208 | SUPERFAMILY | SSF51717 | Dihydropteroate synthetase-like |
| 15 | 208 | InterPro | IPR011005 | Dihydropteroate synthase-like |
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_A0A0H3GRM8
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_4655
|
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 |
|---|---|---|---|---|---|---|---|
| 3 | 0.057 | ||||||
| 1 | 0.001 | ||||||
| 2 | 0.001 | ||||||
| 23 | 0.0 |
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 | 7.57 | 0.335 | ||||||
| 2 | 3.84 | 0.121 | ||||||
| 3 | 3.56 | 0.106 | ||||||
| 4 | 1.61 | 0.021 | ||||||
| 5 | 1.23 | 0.01 |
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 | 0.037 | ||||||
| 2 | 0.013 | ||||||
| 24 | 0.002 | ||||||
| 14 | 0.0 |
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 | 10.09 | 0.467 | ||||||
| 2 | 2.69 | 0.065 | ||||||
| 3 | 1.17 | 0.008 | ||||||
| 4 | 1.12 | 0.007 |
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 | Q5SLI8 | 216.0 Da LogP -0.15 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
C#CCOP(=O)(O)OP(=O)(O)O
|
|
| 43Q | Q5SLI8 | 279.1 Da LogP -0.84 TPSA 153.8 | ✓ Ro5 | ✓ Clean |
C[C+](CO)[C@@H](COP(=O)(O)OP(=O)(O)O)O
|
|
| 43W | Q5SLI8 | 230.0 Da LogP 0.24 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
C#CCCOP(=O)(O)OP(=O)(O)O
|
|
| CDI | Q5SLI8 | 278.1 Da LogP -0.64 TPSA 142.8 | ✓ Ro5 | ✓ Clean |
C[C@@]1([C@@H](CO[P@](=O)(O[P@](=O)(O1)O)O)O)CO
|
|
| DPO | Q5SLI8 | 173.9 Da LogP -3.34 TPSA 135.6 | ✓ Ro5 | ✓ Clean |
[O-]P(=O)([O-])OP(=O)([O-])[O-]
|
|
| F3S | Q5SLI8 | 295.8 Da LogP 2.59 TPSA 0.0 | ✓ Ro5 | ✓ Clean |
S1[Fe]2S[Fe]3[S]2[Fe]1S3
|
|
| H6P | Q5SLI8 | 262.1 Da LogP 0.15 TPSA 133.5 | ✓ Ro5 | ✓ Clean |
C/C(=C\CO[P@@](=O)(O)OP(=O)(O)O)/CO
|
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 |
|---|---|---|---|---|---|
| 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
|
| ZINC8215740 | 0.700 | 246.1 Da LogP 1.18 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
CC(C)=CCO[P@@](=O)(O)OP(=O)(O)O
|
| ZINC8215849 | 0.657 | 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
|
| ZINC71769106 | 0.656 | 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
|
| ZINC12494625 | 0.639 | 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 | 0.639 | 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 | 0.622 | 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 | 0.605 | 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
|
| ZINC39419974 | 0.520 | 212.1 Da LogP 1.04 TPSA 44.8 | ✓ Ro5 | ✓ Clean |
C#CCOP(=O)(OCC#C)OCC#C
|
| ZINC2579357 | 0.500 | 248.1 Da LogP 1.26 TPSA 113.3 | ✓ Ro5 | ✓ Clean |
CC(C)CCO[P@](=O)(O)OP(=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.