Structure of PDB 8pk0 Chain z Binding Site BS02

Receptor Information
>8pk0 Chain z (length=311) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WRENFPLCGRDVARWFPGHMAKGLKKMQSSLKLVDCIIEVHDARIPLSGR
NPLFQETLGLKPHLLVLNKMDLADLTEQQKIMQHLEGEGLKNVIFTNCVK
DENVKQIIPMVTELIGRSHRYHRKENLEYCIMVIGVPNVGKSSLINSLRR
QHLRKGKATRVGGEPGITRAVMSKIQVSERPLMFLLDTPGVLAPRIESVE
TGLKLALCGTVLDHLVGEETMADYLLYTLNKHQRFGYVQHYGLGSACDNV
ERVLKSVAVKLGKTQKVKVLTGTGNVNIIQPNYPAAARDFLQTFRRGLLG
SVMLDLDVLRG
Ligand information
Ligand IDGNP
InChIInChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
InChIKeyUQABYHGXWYXDTK-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
FormulaC10 H17 N6 O13 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
ChEMBLCHEMBL1233085
DrugBankDB02082
ZINCZINC000037868676
PDB chain8pk0 Chain z Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8pk0 Structural insights into the role of GTPBP10 in the RNA maturation of the mitoribosome.
Resolution3.03 Å
Binding residue
(original residue number in PDB)		N83 K84 D86 L87 N112 N153 G155 K156 S157 S158 V176 G177 G181 I182 T183
Binding residue
(residue number reindexed from 1)		N68 K69 D71 L72 N97 N138 G140 K141 S142 S143 V161 G162 G166 I167 T168
Annotation score3
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
Biological Process
GO:0006417 regulation of translation
GO:0032543 mitochondrial translation
GO:0044065 regulation of respiratory system process
GO:0070129 regulation of mitochondrial translation
Cellular Component
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005759 mitochondrial matrix
GO:0005761 mitochondrial ribosome

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8pk0, PDBe:8pk0, PDBj:8pk0
PDBsum8pk0
PubMed38042949
UniProtQ9BT17|MTG1_HUMAN Mitochondrial ribosome-associated GTPase 1 (Gene Name=MTG1)

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