PDB Entry (4phh)
PDB ID: 4phh Resolution: 2.35 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}-3H-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)aminophosphonic acid
Canonical SMILES:   O[C@@H]1[C@@H](COP(O)(=O)OP(O)(=O)NP(O)(O)=O)O[C@H]([C@@H]1O)n1cnc2c1nc(NCCCNC(=O)C=C)[nH]c2=O
Standard InChI:   InChI=1S/C16H26N7O14P3/c1-2-9(24)17-4-3-5-18-16-20-13-10(14(27)21-16)19-7-23(13)15-12(26)11(25)8(36-15)6-35-40(33,34)37-39(31,32)22-38(28,29)30/h2,7-8,11-12,15,25-26H,1,3-6H2,(H,17,24)(H,33,34)(H2,18,20,21,27)(H4,22,28,29,30,31,32)/t8-,11-,12-,15-/m1/s1
HET Code:   2UK PubChem:   -
DrugBank:   - ChEMBL:   -
Molecular Formula:   C16H26N7O14P3 Mol. Weight:   633.0751 logP:   -2.2407
HBD:   10 HBA:   14
#Rotatable Bonds:   14 TPSA:   317.01
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Michael Addition CYS 35 A 88.15 9.52 Vinyl Carbonyl
Binding Affinity
-