Structure of PDB 4dpg Chain C Binding Site BS02
Receptor Information
>4dpg Chain C (length=501) Species:
9606
(Homo sapiens) [
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VDPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDH
LTDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFI
HINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLKDKE
TRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNII
PGGAVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGRQFRN
EGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGSYKVTYH
PDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILD
DICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAK
WHRSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDD
EAMFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLFPAMK
P
Ligand information
Ligand ID
APC
InChI
InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1
InChIKey
CAWZRIXWFRFUQB-IOSLPCCCSA-N
SMILES
Software
SMILES
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)O)N
CACTVS 3.341
Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N
ACDLabs 10.04
O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341
Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
Formula
C11 H18 N5 O12 P3
Name
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
ChEMBL
CHEMBL132722
DrugBank
DB02596
ZINC
ZINC000008295117
PDB chain
4dpg Chain C Residue 602 [
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Receptor-Ligand Complex Structure
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PDB
4dpg
Structural Switch of Lysyl-tRNA Synthetase between Translation and Transcription.
Resolution
2.844 Å
Binding residue
(original residue number in PDB)
R323 T330 H331 N332 F335 R553
Binding residue
(residue number reindexed from 1)
R249 T256 H257 N258 F261 R479
Annotation score
3
Enzymatic activity
Catalytic site (original residue number in PDB)
R323 E325 T330 H331 E494 N497 R553
Catalytic site (residue number reindexed from 1)
R249 E251 T256 H257 E420 N423 R479
Enzyme Commision number
2.7.7.-
6.1.1.6
: lysine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166
nucleotide binding
GO:0003676
nucleic acid binding
GO:0004812
aminoacyl-tRNA ligase activity
GO:0004824
lysine-tRNA ligase activity
GO:0005524
ATP binding
Biological Process
GO:0006418
tRNA aminoacylation for protein translation
GO:0006430
lysyl-tRNA aminoacylation
Cellular Component
GO:0005737
cytoplasm
View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB
RCSB:4dpg
,
PDBe:4dpg
,
PDBj:4dpg
PDBsum
4dpg
PubMed
23159739
UniProt
Q15046
|SYK_HUMAN Lysine--tRNA ligase (Gene Name=KARS1)
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