Structure of PDB 1afk Chain B Binding Site BS01
Receptor Information
>1afk Chain B (length=124) Species:
9913
(Bos taurus) [
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KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHES
LADVQAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTT
QANKHIIVACEGNPYVPVHFDASV
Ligand information
Ligand ID
PAP
InChI
InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(27-29(17,18)19)4(26-10)1-25-31(23,24)28-30(20,21)22/h2-4,6-7,10,16H,1H2,(H,23,24)(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/t4-,6-,7-,10-/m1/s1
InChIKey
GBBWIZKLHXYJOA-KQYNXXCUSA-N
SMILES
Software
SMILES
ACDLabs 10.04
O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
CACTVS 3.341
Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]3O
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(O)O)O)N
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)OP(=O)(O)O)OP(=O)(O)O)O)N
CACTVS 3.341
Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O[P](O)(O)=O)[C@H]3O
Formula
C10 H16 N5 O13 P3
Name
3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE
ChEMBL
DrugBank
DB01842
ZINC
ZINC000013527438
PDB chain
1afk Chain B Residue 125 [
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Receptor-Ligand Complex Structure
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PDB
1afk
Crystal structures of ribonuclease A complexes with 5'-diphosphoadenosine 3'-phosphate and 5'-diphosphoadenosine 2'-phosphate at 1.7 A resolution.
Resolution
1.7 Å
Binding residue
(original residue number in PDB)
A4 K7 Q11 H12 C65 N67 Q69 N71 A109 V118 H119 F120
Binding residue
(residue number reindexed from 1)
A4 K7 Q11 H12 C65 N67 Q69 N71 A109 V118 H119 F120
Annotation score
1
Binding affinity
MOAD
: Ki=240nM
Enzymatic activity
Catalytic site (original residue number in PDB)
H12 K41 H119 F120 D121
Catalytic site (residue number reindexed from 1)
H12 K41 H119 F120 D121
Enzyme Commision number
4.6.1.18
: pancreatic ribonuclease.
Gene Ontology
Molecular Function
GO:0003676
nucleic acid binding
GO:0004519
endonuclease activity
GO:0004522
ribonuclease A activity
GO:0004540
RNA nuclease activity
GO:0005515
protein binding
GO:0016829
lyase activity
Biological Process
GO:0050830
defense response to Gram-positive bacterium
Cellular Component
GO:0005576
extracellular region
View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB
RCSB:1afk
,
PDBe:1afk
,
PDBj:1afk
PDBsum
1afk
PubMed
9154942
UniProt
P61823
|RNAS1_BOVIN Ribonuclease pancreatic (Gene Name=RNASE1)
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