Structure of PDB 5vps Chain A Binding Site BS01

Receptor Information
>5vps Chain A (length=260) Species: 398577 (Burkholderia ambifaria MC40-6) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMDLGIAGKTALVCAASKGLGRGCAEALAAEGVNLVIVARTRDTLEETAE
EIRAASNVSVTAVACDITTPDGRAAALAACPQPDILVNNAGGPPPGDFRD
FSHDDWIRALEANMLTPIELIRATVDGMIGRGFGRIVNITSSAVKAPIDV
LALSNGARSGLTGFVAGLSRKVAGQGVTINNLLPGLFDTDRIATTLAASA
KAQGVTVDELRARRAKEIPAGRLGTRAEFGAACAFLCSVHAGYITGQNWL
LDGGAYPGTF
Ligand information
Ligand ID9G1
InChIInChI=1S/C30H47N7O23P4/c31-26-21-28(34-12-33-26)37(13-35-21)30-25(59-62(48,49)50)23(45)16(58-30)11-56-64(53,54)60-63(51,52)55-10-15-22(44)24(46)29(57-15)36-5-1-17(14(9-36)27(32)47)61(6-2-18(38)39,7-3-19(40)41)8-4-20(42)43/h12-17,22-25,29-30,44-46H,1-11H2,(H10-,31,32,33,34,38,39,40,41,42,43,47,48,49,50,51,52,53,54)/p+1/t14-,15+,16+,17-,22+,23+,24+,25+,29+,30+/m0/s1
InChIKeyKCEMQRAWVXDPSM-NLJDEQFRSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5CCC(C(C5)C(=O)N)[P+](CCC(=O)O)(CCC(=O)O)CCC(=O)O)O)O)O)OP(=O)(O)O)N
CACTVS 3.385NC(=O)[C@H]1CN(CC[C@@H]1[P+](CCC(O)=O)(CCC(O)=O)CCC(O)=O)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5CC[C@@H](C(C5)C(=O)N)[P+](CCC(=O)O)(CCC(=O)O)CCC(=O)O)O)O)O)OP(=O)(O)O)N
CACTVS 3.385NC(=O)[CH]1CN(CC[CH]1[P+](CCC(O)=O)(CCC(O)=O)CCC(O)=O)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
FormulaC30 H48 N7 O23 P4
Name[(4~{S})-3-aminocarbonyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]piperidin-4-yl]-tris(3-hydroxy-3-oxopropyl)phosphanium
ChEMBL
DrugBank
ZINC
PDB chain5vps Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vps Cautionary Tale of Using Tris(alkyl)phosphine Reducing Agents with NAD+-Dependent Enzymes.
Resolution1.45 Å
Binding residue
(original residue number in PDB)
A14 S16 G18 L19 A38 R39 T40 D65 I66 N88 A89 G90 G91 S140 S141 L150 S153 R157 P183 G184 L185 F186 T188 R190 I191 T194
Binding residue
(residue number reindexed from 1)
A15 S17 G19 L20 A39 R40 T41 D66 I67 N89 A90 G91 G92 S141 S142 L151 S154 R158 P184 G185 L186 F187 T189 R191 I192 T195
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) N137 S153 R157 A197
Catalytic site (residue number reindexed from 1) N138 S154 R158 A198
Enzyme Commision number ?
External links