Structure of PDB 3pd4 Chain B Binding Site BS01

Receptor Information
>3pd4 Chain B (length=143) Species: 29292 (Pyrococcus abyssi) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVLLIHSDYIEYEVKDKALKNPEPISEDMKRGRMEEVLVAFISVEKVDE
KNPEEVSLKAIEEISKVAEQVKAENVFVYPFAHLSSELAKPSVAMDILNR
VYQGLKERGFNVGKAPFGYYKAFKISCKGHPLAELSRTIVPEE
Ligand information
Ligand IDA3G
InChIInChI=1S/C12H17N7O4/c13-1-6(21)18-7-5(2-20)23-12(9(7)22)19-4-17-8-10(14)15-3-16-11(8)19/h3-5,7,9,12,20,22H,1-2,13H2,(H,18,21)(H2,14,15,16)/t5-,7-,9-,12-/m1/s1
InChIKeyXJJYXFHVLHMVGL-MUIQIWNUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NCC(=O)N[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(NC3C(OC(n2cnc1c(ncnc12)N)C3O)CO)CN
CACTVS 3.370NCC(=O)N[CH]1[CH](O)[CH](O[CH]1CO)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)NC(=O)CN)O)N
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)NC(=O)CN)O)N
FormulaC12 H17 N7 O4
Name3'-deoxy-3'-(glycylamino)adenosine
ChEMBL
DrugBank
ZINCZINC000058631680
PDB chain3pd4 Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3pd4 Mechanistic insights into cognate substrate discrimination during proofreading in translation
Resolution2.4 Å
Binding residue
(original residue number in PDB)		A19 L20 V45 F81 F117 G118 Y119
Binding residue
(residue number reindexed from 1)		A19 L20 V45 F81 F117 G118 Y119
Annotation score2
Binding affinityMOAD: Kd=33.3uM
PDBbind-CN: -logKd/Ki=4.48,Kd=33.2uM
Enzymatic activity
Enzyme Commision number 6.1.1.3: threonine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0004829 threonine-tRNA ligase activity
GO:0005524 ATP binding
GO:0008270 zinc ion binding
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:3pd4, PDBe:3pd4, PDBj:3pd4
PDBsum3pd4
PubMed21098258
UniProtQ9UZ14|SYT_PYRAB Threonine--tRNA ligase (Gene Name=thrS)

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