Structure of PDB 4nbi Chain A Binding Site BS01

Receptor Information
>4nbi Chain A (length=163) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWE
DALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNK
PDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGP
VTIYIDTHDINLN
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 chain4nbi Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4nbi Mechanism of chiral proofreading during translation of the genetic code.
Resolution1.86 Å
Binding residue
(original residue number in PDB)		I43 S87 Q88 F89 K107 A112 F137 G138
Binding residue
(residue number reindexed from 1)		I43 S87 Q88 F89 K107 A112 F137 G138
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Q88 F89 T90
Catalytic site (residue number reindexed from 1) Q88 F89 T90
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4nbi, PDBe:4nbi, PDBj:4nbi
PDBsum4nbi
PubMed24302572
UniProtQ8IIS0|DTD_PLAF7 D-aminoacyl-tRNA deacylase (Gene Name=DTD)

[Back to BioLiP]