Structure of PDB 3hio Chain A Binding Site BS01

Receptor Information
>3hio Chain A (length=259) Species: 3988 (Ricinus communis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPIN
QRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAI
THLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYY
STGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSV
ITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIAL
MVYRCAPPP
Ligand information
Ligand IDC2X
InChIInChI=1S/C51H72N21O29P5/c1-85-37-34-26(95-48(37)71-21-62-32-43(71)64-50(54)66-45(32)73)15-91-102(75,76)89-9-7-5-4-6-8-88-68-101-106(83,84)100-36-28(94-47(39(36)87-3)70-20-61-31-41(53)59-19-60-42(31)70)17-93-105(81,82)99-35-27(96-49(38(35)86-2)72-22-63-33-44(72)65-51(55)67-46(33)74)16-92-103(77,78)97-25-13-69(12-24(25)14-90-104(79,80)98-34)11-23-10-56-30-29(23)57-18-58-40(30)52/h10,18-22,24-28,34-39,47-49,56,68H,4-9,11-17H2,1-3H3,(H,75,76)(H,77,78)(H,79,80)(H,81,82)(H,83,84)(H2,52,57,58)(H2,53,59,60)(H3,54,64,66,73)(H3,55,65,67,74)/t24-,25+,26-,27-,28-,34-,35-,36-,37-,38-,39-,47-,48-,49-/m1/s1
InChIKeyUYGVCRAKTIGHOS-DFLHJNKYSA-N
SMILES
SoftwareSMILES
CO[C@@H]1[C@@H]2O[P@](O)(=O)OC[C@H]3CN(C[C@@H]3O[P@](O)(=O)OC[C@H]4O[C@H]([C@H](OC)[C@@H]4O[P@](O)(=O)OC[C@H]5O[C@H]([C@H](OC)[C@@H]5O[P@@](O)(=O)ONOCCCCCCO[P@](O)(=O)OC[C@H]2O[C@H]1n6cnc7C(=O)N=C(N)Nc67)n8cnc9c(N)ncnc89)n%10cnc%11C(=O)N=C(N)Nc%10%11)Cc%12c[nH]c%13c(N)ncnc%12%13
ACDLabs 10.04O=P7(O)OCC%13OC(n1c2ncnc(c2nc1)N)C(OC)C%13OP(=O)(O)ONOCCCCCCOP(=O)(O)OCC%12OC(n3c4NC(=NC(=O)c4nc3)N)C(OC)C%12OP(=O)(O)OCC%11C(OP(=O)(O)OCC8OC(n5c6NC(=NC(=O)c6nc5)N)C(OC)C8O7)CN(Cc%10c9ncnc(c9nc%10)N)C%11
CO[CH]1[CH]2O[P](O)(=O)OC[CH]3CN(C[CH]3O[P](O)(=O)OC[CH]4O[CH]([CH](OC)[CH]4O[P](O)(=O)OC[CH]5O[CH]([CH](OC)[CH]5O[P](O)(=O)ONOCCCCCCO[P](O)(=O)OC[CH]2O[CH]1n6cnc7C(=O)N=C(N)Nc67)n8cnc9c(N)ncnc89)n%10cnc%11C(=O)N=C(N)Nc%10%11)Cc%12c[nH]c%13c(N)ncnc%12%13
OpenEye OEToolkits 1.5.0COC1C2C(COP(=O)(OCCCCCCONOP(=O)(OC3C(COP(=O)(OC4C(COP(=O)(OC5CN(CC5COP(=O)(O2)O)Cc6c[nH]c7c6ncnc7N)O)OC(C4OC)n8cnc9c8NC(=NC9=O)N)O)OC(C3OC)n2cnc3c2ncnc3N)O)O)OC1n1cnc2c1NC(=NC2=O)N
CO[C@@H]1[C@H]2[C@@H](CO[P@@](=O)(OCCCCCCONO[P@](=O)(O[C@@H]3[C@@H](CO[P@@](=O)(O[C@@H]4[C@@H](CO[P@@](=O)(O[C@H]5CN(C[C@@H]5CO[P@@](=O)(O2)O)Cc6c[nH]c7c6ncnc7N)O)O[C@H]([C@@H]4OC)n8cnc9c8NC(=NC9=O)N)O)O[C@H]([C@@H]3OC)n2cnc3c2ncnc3N)O)O)O[C@H]1n1cnc2c1NC(=NC2=O)N
FormulaC51 H72 N21 O29 P5
Name9,9'-{(2R,3R,3aR,5S,7aR,9R,10R,10aR,12S,23R,25aR,27R,28R,28aR,30S,32aR,35aR,37S,39aR)-9-(6-amino-9H-purin-9-yl)-34-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-5,12,23,30,37-pentahydroxy-3,10,28-trimethoxy-5,12,23,30,37-pentaoxidotetracosahydro-2H,7H,25H-trifuro[3,2-f:3',2'-l:3'',2''-x]pyrrolo[3,4-r][1,3,5,9,11,15,17,21,23,27,29,2,4,10,16,22,28]undecaoxazapentaphosphacyclopentatriacontine-2,27-diyl}bis(2-amino-3,9-dihydro-6H-purin-6-one)
ChEMBL
DrugBank
ZINC
PDB chain3hio Chain A Residue 268 [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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PDB3hio Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins.
Resolution2.0 Å
Binding residue
(original residue number in PDB)
D75 N78 Y80 V81 D96 D100 G121 Y123 I172 R180 W211 G212 R213 R258
Binding residue
(residue number reindexed from 1)
D71 N74 Y76 V77 D92 D96 G117 Y119 I168 R176 W207 G208 R209 R254
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.52,Ki=300nM
Enzymatic activity
Catalytic site (original residue number in PDB) V81 E177 R180
Catalytic site (residue number reindexed from 1) V77 E173 R176
Enzyme Commision number 3.2.2.22: rRNA N-glycosylase.
Gene Ontology
Molecular Function
GO:0030598 rRNA N-glycosylase activity
Biological Process
GO:0017148 negative regulation of translation

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Molecular Function

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Biological Process
External links
PDB RCSB:3hio, PDBe:3hio, PDBj:3hio
PDBsum3hio
PubMed19920175
UniProtP02879|RICI_RICCO Ricin

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