Structure of PDB 4nbj Chain D Binding Site BS02

Receptor Information
>4nbj Chain D (length=154) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVVIQRVKGAILSVRKELEIISEIKNGLICFLGIHKNDTWEDALYIIRK
CLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKE
PNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTH
DINL
Ligand information
Ligand IDD3Y
InChIInChI=1S/C19H23N7O5/c20-11(5-9-1-3-10(28)4-2-9)18(30)25-13-12(6-27)31-19(15(13)29)26-8-24-14-16(21)22-7-23-17(14)26/h1-4,7-8,11-13,15,19,27-29H,5-6,20H2,(H,25,30)(H2,21,22,23)/t11-,12-,13-,15-,19-/m1/s1
InChIKeyGCCJIIJWAJOTAC-XDJZACDYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385N[C@H](Cc1ccc(O)cc1)C(=O)N[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO)n3cnc4c(N)ncnc34
CACTVS 3.385N[CH](Cc1ccc(O)cc1)C(=O)N[CH]2[CH](O)[CH](O[CH]2CO)n3cnc4c(N)ncnc34
OpenEye OEToolkits 1.7.6c1cc(ccc1CC(C(=O)NC2C(OC(C2O)n3cnc4c3ncnc4N)CO)N)O
ACDLabs 12.01O=C(NC3C(OC(n2cnc1c(ncnc12)N)C3O)CO)C(N)Cc4ccc(O)cc4
OpenEye OEToolkits 1.7.6c1cc(ccc1C[C@H](C(=O)N[C@@H]2[C@H](O[C@H]([C@@H]2O)n3cnc4c3ncnc4N)CO)N)O
FormulaC19 H23 N7 O5
Name3'-deoxy-3'-(D-tyrosylamino)adenosine
ChEMBL
DrugBank
ZINCZINC000095920739
PDB chain4nbj Chain D Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4nbj Mechanism of chiral proofreading during translation of the genetic code.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		I43 S87 Q88 F89 K107 F137 G138 Y140
Binding residue
(residue number reindexed from 1)		I35 S79 Q80 F81 K99 F129 G130 Y132
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Q88 F89 T90
Catalytic site (residue number reindexed from 1) Q80 F81 T82
Enzyme Commision number 3.1.1.96: D-aminoacyl-tRNA deacylase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0002161 aminoacyl-tRNA editing activity
GO:0016787 hydrolase activity
GO:0051499 D-aminoacyl-tRNA deacylase activity
GO:0051500 D-tyrosyl-tRNA(Tyr) deacylase activity
GO:0106026 Gly-tRNA(Ala) hydrolase activity
Biological Process
GO:0006399 tRNA metabolic process
GO:0106074 aminoacyl-tRNA metabolism involved in translational fidelity
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4nbj, PDBe:4nbj, PDBj:4nbj
PDBsum4nbj
PubMed24302572
UniProtQ8IIS0|DTD_PLAF7 D-aminoacyl-tRNA deacylase (Gene Name=DTD)

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