PDB Entry (4phg)
PDB ID: 4phg Resolution: 1.9 Å Exp. Method: X-RAY DIFFRACTION
PMID: 26178622 DOI: 10.1038/ncomms8773
Protein
Protein Name: Ypt/Rab-type GTPase YPT7
Uniprot ID/ACC: P32939 (YPT7_YEAST) Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Gene Symbol: YPT7 Gene ID: 855012
Protein Class: HYDROLASE
Ligand
Ligand Name:   ({[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(6-oxo-2-{[3-(prop-2-enamido)propyl]amino}-6,9-dihydro-3H-purin-9-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acid
Canonical SMILES:   O[C@@H]1[C@@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)O[C@H]([C@@H]1O)n1cnc2c1nc(NCCCNC(=O)C=C)[nH]c2=O
Standard InChI:   InChI=1S/C16H25N6O15P3/c1-2-9(23)17-4-3-5-18-16-20-13-10(14(26)21-16)19-7-22(13)15-12(25)11(24)8(35-15)6-34-39(30,31)37-40(32,33)36-38(27,28)29/h2,7-8,11-12,15,24-25H,1,3-6H2,(H,17,23)(H,30,31)(H,32,33)(H2,27,28,29)(H2,18,20,21,26)/t8-,11-,12-,15-/m1/s1
HET Code:   2UJ PubChem:   -
DrugBank:   - ChEMBL:   -
Molecular Formula:   C16H25N6O15P3 Mol. Weight:   634.0591 logP:   -1.8137
HBD:   9 HBA:   15
#Rotatable Bonds:   14 TPSA:   314.21
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Michael Addition CYS 35 A 101.4 - Vinyl Carbonyl
Binding Affinity
-