Structure of PDB 5i34 Chain A Binding Site BS01

Receptor Information
>5i34 Chain A (length=429) Species: 235443 (Cryptococcus neoformans var. grubii H99) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APSPEGVTVVLGAQWGDEGKGKLVDILAAEADICARCAGGNNAGHTIVVR
NDKGEKTSYAFNLLPSGLINPECTAFIGSGVVVHVPSLFNELDTLERKGL
KVAGRLLVSDRAHLVMGFHQIVDGLKEVELGGSSIGTTRKGIGPAYSSKA
SRSGLRVHHLFDPTFPAKFRKLVEGRFKRYGHFEFDTEGEIEMYLAFAER
LRPFIVDGPTFMHNALSSGKRVLVEGANALMLDLDYGTYPFVTSSSTSIG
GVVSGLGISPFAIKRVVGVIKAYTTRVGGGPFPTEDLATVGETLQEVGAE
YGTVTGRRRRCGWLDLVVMKYSTMINGYTSLNLTKLDVLDGFEEIKVATG
YKIDGVEVEGFPADLDRLAKVEVQYATLPGWKTDISNCKTYEEFPENAKA
YIKFIEDYLGVKVQYVGVGPGRDQNVIIF
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 chain5i34 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5i34 Disruption of de Novo Adenosine Triphosphate (ATP) Biosynthesis Abolishes Virulence in Cryptococcus neoformans.
Resolution1.53 Å
Binding residue
(original residue number in PDB)		G20 K21 G22 K23 H46 K336 D338 G418 G420 P421
Binding residue
(residue number reindexed from 1)		G19 K20 G21 K22 H45 K335 D337 G417 G419 P420
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D18 K21 G45 H46 N229
Catalytic site (residue number reindexed from 1) D17 K20 G44 H45 N228
Enzyme Commision number 6.3.4.4: adenylosuccinate synthase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0004019 adenylosuccinate synthase activity
GO:0005525 GTP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0006164 purine nucleotide biosynthetic process
GO:0006167 AMP biosynthetic process
GO:0044208 'de novo' AMP biosynthetic process
GO:0046040 IMP metabolic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5i34, PDBe:5i34, PDBj:5i34
PDBsum5i34
PubMed27759389
UniProtJ9VI09

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