Structure of PDB 7jfp Chain B Binding Site BS01

Receptor Information
>7jfp Chain B (length=393) Species: 9823 (Sus scrofa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNLQEYQSKKLMSDNGVKVQRFFVADTANEALEAAKRLNAKEIVLKAQIL
AGGRGKGVFSSGLKGGVHLTKDPEVVGQLAKQMIGYNLATKQTPKEGVKV
NKVMVAEALDISRETYLAILMDRSCNGPVLVGSPQGGVDIEEVAASNPEL
IFKEQIDIIEGIKDSQAQRMAENLGFLGPLQNQAADQIKKLYNLFLKIDA
TQVEVNPFGETPEGQVVCFDAKINFDDNAEFRQKDIFAMDDKSENEPIEN
EAAKYDLKYIGLDGNIACFVNGAGLAMATCDIIFLNGGKPANFLDLGGGV
KESQVYQAFKLLTADPKVEAILVNIFGGIVNCAIIANGITKACRELELKV
PLVVRLEGTNVHEAQNILTNSGLPITSAVDLEDAAKKAVASVT
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 chain7jfp Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7jfp Second distinct conformation of the phosphohistidine loop in succinyl-CoA synthetase
Resolution2.55 Å
Binding residue
(original residue number in PDB)		R54 L109 I111 E114 V138 F219 D220 K222
Binding residue
(residue number reindexed from 1)		R54 L109 I111 E114 V138 F219 D220 K222
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y116 E204
Catalytic site (residue number reindexed from 1) Y116 E204
Enzyme Commision number 6.2.1.4: succinate--CoA ligase (GDP-forming).
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004775 succinate-CoA ligase (ADP-forming) activity
GO:0004776 succinate-CoA ligase (GDP-forming) activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0006099 tricarboxylic acid cycle
GO:0006104 succinyl-CoA metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0042709 succinate-CoA ligase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7jfp, PDBe:7jfp, PDBj:7jfp
PDBsum7jfp
PubMed
UniProtP53590|SUCB2_PIG Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial (Fragment) (Gene Name=SUCLG2)

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