Structure of PDB 4nxv Chain A Binding Site BS01

Receptor Information
>4nxv Chain A (length=330) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RMSLQEKLLTYYRNRAAIPAGEQARAKQAAVDICAELRSFLRAKLPDMPL
RDMYLSGSLYDDLQVVTADHIQLIVPLVLEQNLWSCIPGEDTIMNVPGFF
LVRRENPEYFPRGSSYWDRCVVGGYLSPKTVADTFEKVVAGSINWPAIGS
LLDYVIRPAPPEALTLEVQYERDKHLFIDFLPSVTLGDTVLVAKPHRLAQ
YDNLWRLSLRPAETARLRALDQADSGCRSLCLKILKAICKSTPALGHLTA
SQLTNVILHLAQEEADWSPDMLADRFLQALRGLISYLEAGVLPSALNPKV
NLFAELTPEEIDELGYTLYCSLSEPEVLLQ
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain4nxv Chain A Residue 501 [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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PDB4nxv Structural and functional analysis of MiD51, a dynamin receptor required for mitochondrial fission.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		S189 H201 Q203 K326 S340 R342 K368 A382
Binding residue
(residue number reindexed from 1)		S58 H70 Q72 K194 S208 R210 K236 A250
Annotation score4
Binding affinityMOAD: Kd=3.8uM
PDBbind-CN: -logKd/Ki=5.42,Kd=3.8uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Biological Process
GO:0007005 mitochondrion organization
Cellular Component
GO:0005741 mitochondrial outer membrane

View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4nxv, PDBe:4nxv, PDBj:4nxv
PDBsum4nxv
PubMed24515348
UniProtQ9NQG6|MID51_HUMAN Mitochondrial dynamics protein MIEF1 (Gene Name=MIEF1)

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