Structure of PDB 7vyp Chain B Binding Site BS02

Receptor Information
>7vyp Chain B (length=674) Species: 1912 (Streptomyces hygroscopicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLVLGLNGNFSAADTDVVPQLGEVFFHDSAASLIRDGELVAAVEEERLNR
IKKTTKFPLNAVRECLALAGARPEDVDAVGYYFPENHIDTVLNHLYTEYP
RAPLRYSRELIRQRLKEGLGWDLPDEKLVYVPHHEAHAYSSYLHSGMDSA
LVLVLDGRGELHSGTVYRAEGTRLEKLADYPVPKSLGGLYLNATYLLGYG
FGDEYKVMGLAPWGNPETYRDTFAKLYTLQDNGEYELHGNIMVPNLVSPL
FYAEGFRPRRKGEPFTQAHRDFAAALQETVEKIVLHILEYWAKTSGHSRL
CFGGGVAHNSSLNGLILKSGLFDEVFVHPASHDAGAGEGAAYAAAASLGT
LERPGKRLLSASLGPALGGREQIRARLADWAPLIDVEFPDDAVETAAGLL
AEGQVLGWAYGRSEFGPRALGHRSIVADARPEENRTRINAMVKKREGFRP
FAPVVTAEAARDYFDLSGADGNHEFMSFVVPVLPERRTELGAVTHVDGTA
RVQVVSAESGERFHRLVRRFGELTGTPVLLNTSFNNNAEPIVQSLDDVVT
SFLTTDLDVLVVEDCLVRGKASPDLGVLVPRFRPVTRLVERRTAGPDASA
GAKTHEIHLDYDGGPSAKVSPELYELLGAVDGTTTLGDLAKTVGGLSDAL
ATEVFALWEQRFLTLAPAGDIGPL
Ligand information
Ligand ID8CW
InChIInChI=1S/C37H49ClN7O14P/c1-18-7-6-8-25(54-4)24(47)13-26(20(3)10-19(2)23(46)14-29(48)44-22-11-21(9-18)12-27(55-5)30(22)38)58-37(40,51)59-60(52,53)56-15-28-32(49)33(50)36(57-28)45-17-43-31-34(39)41-16-42-35(31)45/h6-8,10-12,16-17,20,23,25-26,28,32-33,36,46,49-51H,9,13-15,40H2,1-5H3,(H,44,48)(H,52,53)(H2,39,41,42)/b8-6+,18-7+,19-10+/t20-,23-,25+,26-,28+,32+,33+,36+,37-/m0/s1
InChIKeyQLSIIXOKLGYKPW-VYDMNOPCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C[C@H]1/C=C(/[C@H](CC(=O)Nc2cc(cc(c2Cl)OC)C/C(=C/C=C/[C@H](C(=O)C[C@@H]1O[C@](N)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)OC)/C)O)\C
OpenEye OEToolkits 2.0.7CC1C=C(C(CC(=O)Nc2cc(cc(c2Cl)OC)CC(=CC=CC(C(=O)CC1OC(N)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)OC)C)O)C
CACTVS 3.385CO[C@@H]1/C=C/C=C(\C)Cc2cc(NC(=O)C[C@H](O)C(=C/[C@H](C)[C@H](CC1=O)O[C@](N)(O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)/C)c(Cl)c(OC)c2
CACTVS 3.385CO[CH]1C=CC=C(C)Cc2cc(NC(=O)C[CH](O)C(=C[CH](C)[CH](CC1=O)O[C](N)(O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)C)c(Cl)c(OC)c2
FormulaC37 H49 Cl N7 O14 P
Name[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl [(~{S})-azanyl-[[(5~{S},6~{E},8~{S},9~{S},12~{R},13~{E},15~{E})-21-chloranyl-12,20-dimethoxy-6,8,16-trimethyl-5-oxidanyl-3,11-bis(oxidanylidene)-2-azabicyclo[16.3.1]docosa-1(21),6,13,15,18(22),19-hexaen-9-yl]oxy]-oxidanyl-methyl] hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain7vyp Chain B Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7vyp Endowing homodimeric carbamoyltransferase GdmN with iterative functions through structural characterization and mechanistic studies.
Resolution2.88 Å
Binding residue
(original residue number in PDB)
V24 F25 F26 H27 H87 V91 H94 D156 G157 R158 G187 Y190 L191 E204 G305 H308 N309 H332 D333
Binding residue
(residue number reindexed from 1)
V24 F25 F26 H27 H87 V91 H94 D156 G157 R158 G187 Y190 L191 E204 G305 H308 N309 H332 D333
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0046872 metal ion binding
Biological Process
GO:0009058 biosynthetic process

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Molecular Function

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Biological Process
External links
PDB RCSB:7vyp, PDBe:7vyp, PDBj:7vyp
PDBsum7vyp
PubMed36329057
UniProtQ84G19

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