Structure of PDB 2fpg Chain B Binding Site BS01

Receptor Information
>2fpg 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 chain2fpg Chain B Residue 397 [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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PDB2fpg Interactions of GTP with the ATP-grasp Domain of GTP-specific Succinyl-CoA Synthetase
Resolution2.96 Å
Binding residue
(original residue number in PDB)		Q20 G52 G53 R54 G55 V67 L69 L109
Binding residue
(residue number reindexed from 1)		Q20 G52 G53 R54 G55 V67 L69 L109
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:2fpg, PDBe:2fpg, PDBj:2fpg
PDBsum2fpg
PubMed16481318
UniProtP53590|SUCB2_PIG Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial (Fragment) (Gene Name=SUCLG2)

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