Structure of PDB 2jbv Chain A Binding Site BS01

Receptor Information
>2jbv Chain A (length=527) Species: 1665 (Arthrobacter globiformis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MHIDNIENLSDREFDYIVVGGGSAGAAVAARLSEDPAVSVALVEAGPDDR
GVPEVLQLDRWMELLESGYDWDYPIEPQENGNSFMRHARAKVMGGCSSHN
SCIAFWAPREDLDEWEAKYGATGWNAEAAWPLYKRLETNEDAGPDAPHHG
DSGPVHLMNVPPKDPTGVALLDACEQAGIPRAKFNTGTTVVNGANFFQIN
RRADGTRSSSSVSYIHPIVEQENFTLLTGLRARQLVFDADRRCTGVDIVD
SAFGHTHRLTARNEVVLSTGAIDTPKLLMLSGIGPAAHLAEHGIEVLVDS
PGVGEHLQDHPEGVVQFEAKQPMVAESTQWWEIGIFTPTEDGLDRPDLMM
HYGSVPFDMNTLRHGYPTTENGFSLTPNVTHARSRGTVRLRSRDFRDKPM
VDPRYFTDPEGHDMRVMVAGIRKAREIAAQPAMAEWTGRELSPGVEAQTD
EELQDYIRKTHNTVYHPVGTVRMGAVEDEMSPLDPELRVKGVTGLRVADA
SVMPEHVTVNPNITVMMIGERCADLIR
Ligand information
Ligand IDFAO
InChIInChI=1S/C27H37N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,18-21,24,26,32,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H2,33,34,42,43)/t14-,15+,16+,18-,19-,20+,21+,24+,26+/m0/s1
InChIKeyVSWYNLHGQAGAHX-AWYOOINRSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N[C@H]3[C@H](NC(=O)NC3=O)N(C[C@H](O)[C@H](O)[C@H](O)CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)[N@@]([C@@H]3[C@H](N2)C(=O)NC(=O)N3)C[C@@H]([C@@H]([C@@H](CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
ACDLabs 10.04O=C2NC(=O)NC3N(c1cc(c(cc1NC23)C)C)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3C(N2)C(=O)NC(=O)N3)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N[CH]3[CH](NC(=O)NC3=O)N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
FormulaC27 H37 N9 O15 P2
Name
ChEMBL
DrugBank
ZINCZINC000098208866
PDB chain2jbv Chain A Residue 1528 [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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PDB2jbv Role of Glu312 in Binding and Positioning of the Substrate for the Hydride Transfer Reaction in Choline Oxidase.
Resolution1.86 Å
Binding residue
(original residue number in PDB)		G22 S23 E44 A45 W71 A90 G95 C96 H99 N100 S101 I103 R231 A232 T269 G270 D273 V464 Y465 H466 D499 A500 N510 P511 N512 V515
Binding residue
(residue number reindexed from 1)		G22 S23 E44 A45 W71 A90 G95 C96 H99 N100 S101 I103 R231 A232 T269 G270 D273 V464 Y465 H466 D499 A500 N510 P511 N512 V515
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.54,Kd=0.29mM
Enzymatic activity
Catalytic site (original residue number in PDB) I333 P377 N378 V464 H466 V509 N510
Catalytic site (residue number reindexed from 1) I333 P377 N378 V464 H466 V509 N510
Enzyme Commision number 1.1.3.17: choline oxidase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
GO:0033713 choline:oxygen 1-oxidoreductase activity
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0019285 glycine betaine biosynthetic process from choline

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2jbv, PDBe:2jbv, PDBj:2jbv
PDBsum2jbv
PubMed18072756
UniProtQ7X2H8|CHOX_ARTGO Choline oxidase (Gene Name=codA)

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