Protein profile

PA3627

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

Genome: NC_002516.2

Gene: ygbB Structure source: ColabFold
Amino acids 157
Annotations 2
Features 16
PDB binders 33
Druggability 0.693

Overview

Basic information about this protein and its source genome.

Accession
PA3627
Gene
ygbB
Status
annotated
Amino acids
157
Structure source
ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
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 0.693
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MRIGHGYDVHRFGEGDFITLGGVRIPHKHGLVAHSDGDVLLHALSDALLGAAALGDIGKHFPDTDPRFKGADSRALLRHVVAIVAEKGWKVGNVDATIVAQAPKMAPHIETMRGLIAEDLGVAVDQVNVKATTTERLGFTGREEGIAVHAVALLMAR

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

2
  • 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:0008685 Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
1 157 Gene3D G3DSA:3.30.1330.50 -
1 157 InterPro IPR036571 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily
2 154 CDD cd00554 MECDP_synthase
2 154 InterPro IPR003526 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
1 156 PANTHER PTHR43181 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE, CHLOROPLASTIC
1 156 InterPro IPR003526 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
35 50 ProSitePatterns PS01350 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.
35 50 InterPro IPR020555 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, conserved site
2 155 NCBIfam TIGR00151 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
2 155 InterPro IPR003526 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
1 157 FunFam G3DSA:3.30.1330.50:FF:000001 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
1 155 SUPERFAMILY SSF69765 IpsF-like
1 155 InterPro IPR036571 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily
1 156 Hamap MF_00107 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [ispF].
1 154 Pfam PF02542 YgbB family
1 154 InterPro IPR003526 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

Loading 3D structure...

Legend High Medium Low

Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
ColabFold PA3627
ColabFold 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
1 0.693
2 0.351

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.

84 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
1AA P62617 566.4 Da LogP -0.87 TPSA 265.2 3 viol. ✓ Clean c1ccc(c(c1)C(=O)OCCO[P@@](=O)(O)O[P@@](=O)(O)OC…
2AA P62617 679.5 Da LogP -0.11 TPSA 262.3 3 viol. ✓ Clean CN(C)c1cccc2c1cccc2S(=O)(=O)NCCO[P@@](=O)(O)O[P…
535 Q3JRA0 210.3 Da LogP 1.88 TPSA 43.6 ✓ Ro5 ✓ Clean CCOC(=O)c1c(n2ccnc2s1)C
6ZB A0A069B2G5 219.2 Da LogP 0.54 TPSA 91.1 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)NO)N
717 Q3JRA0 154.2 Da LogP 0.89 TPSA 37.5 ✓ Ro5 ✓ Clean c1csc2n1cc(n2)CO
795 Q3JRA0 190.2 Da LogP 2.02 TPSA 42.9 ✓ Ro5 ✓ Clean c1cc(cnc1)c2nc(cs2)C=O
829 Q3JRA0 347.3 Da LogP -1.73 TPSA 152.6 ✓ Ro5 ✓ Clean c1cnccc1C(=O)NC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C…
AZM Q3JRA0 222.3 Da LogP -0.86 TPSA 115.0 ✓ Ro5 ✓ Clean CC(=O)Nc1nnc(s1)S(=O)(=O)N
C6B P62617 323.2 Da LogP -2.45 TPSA 177.4 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)[C@@H]2[C@@H]([C@@H]([C@@H](O2…
CAR P62617 323.2 Da LogP -2.45 TPSA 177.4 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2[C@H]([C@@H]([C@H](O2)CO…
CC7 P62617 305.2 Da LogP -1.40 TPSA 146.1 ✓ Ro5 ✓ Clean C1[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=NC3=O)N)…
CDI P62617 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
CDM P62617 521.3 Da LogP -3.20 TPSA 273.6 3 viol. ✓ Clean C[C@](CO)([C@@H](CO[P@](=O)(O)O[P@](=O)(O)OC[C@…
CFV P62617 279.2 Da LogP -1.66 TPSA 147.9 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)C[C@H](CO)OCP(=O)(O)O
CTN Q3JRA0 243.2 Da LogP -2.56 TPSA 130.8 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
CYT Q3JRA0 111.1 Da LogP -0.65 TPSA 71.8 ✓ Ro5 ✓ Clean C1=C(NC(=O)N=C1)N
EZL Q3JRA0 258.3 Da LogP 1.34 TPSA 82.3 ✓ Ro5 ✓ Clean CCOc1ccc2c(c1)sc(n2)S(=O)(=O)N
F01 P62617 261.2 Da LogP -2.42 TPSA 130.8 ✓ Ro5 ✓ Clean C1=C(C(=NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)CO…
F69 Q3JRA0 190.3 Da LogP 2.91 TPSA 20.2 ✓ Ro5 ✓ Clean c1ccc(c(c1)CO)c2cccs2
FPP Q8EBR3 382.3 Da LogP 4.63 TPSA 113.3 ✓ Ro5 ✓ Clean CC(=CCC/C(=C/CC/C(=C/CO[P@@](=O)(O)OP(=O)(O)O)/…
GPP P62617 314.2 Da LogP 2.91 TPSA 113.3 ✓ Ro5 ✓ Clean CC(=CCC/C(=C/CO[P@@](=O)(O)OP(=O)(O)O)/C)C
HHV Q3JRA0 217.2 Da LogP 0.52 TPSA 96.7 ✓ Ro5 ✓ Clean c1cc(cnc1)CNc2c(cn[nH]2)C(=O)N
I5A Q3JRA0 353.1 Da LogP -1.12 TPSA 110.6 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
K4Y Q3JRA0 280.3 Da LogP 0.87 TPSA 107.2 ✓ Ro5 ✓ Clean COc1cc(ncn1)NS(=O)(=O)c2ccc(cc2)N
MLA Q3JRA0 104.1 Da LogP -0.45 TPSA 74.6 ✓ Ro5 ✓ Clean C(C(=O)O)C(=O)O
MLI Q3JRA0 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
MLT Q3JRA0 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
MSR Q3JRA0 160.2 Da LogP 1.58 TPSA 38.0 ✓ Ro5 ✓ Clean c1cc(ccc1n2ccnc2)O
POP Q8ZMF7 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
QMS Q3JRA0 222.3 Da LogP 1.61 TPSA 59.1 ✓ Ro5 ✓ Clean CS(=O)(=O)Nc1cccc2c1nccc2
QOG Q3JRA0 265.3 Da LogP -0.28 TPSA 127.1 ✓ Ro5 ✓ Clean CC(C)NC(=O)Nc1nnc(s1)S(=O)(=O)N
SFY Q3JRA0 249.3 Da LogP 1.46 TPSA 85.1 ✓ Ro5 ✓ Clean c1ccnc(c1)NS(=O)(=O)c2ccc(cc2)N
SUD P62617 601.3 Da LogP -3.08 TPSA 320.1 3 viol. ✓ Clean C[C@](CO)([C@@H](CO[P@](=O)(O)O[P@](=O)(O)OC[C@…

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.