Structure of PDB 1qf4 Chain A Binding Site BS04

Receptor Information
>1qf4 Chain A (length=431) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GNNVVVLGTQWGDEGKGKIVDLLTERAKYVVRYQGGHNAGHTLVINGEKT
VLHLIPSGILRENVTSIIGNGVVLSPAALMKEMKELEDRGIPVRERLLLS
EACPLILDYHVALDNAREKARGAKAIGTTGRGIGPAYEDKVARRGLRVGD
LFDKETFAEKLKEVMEYHNFQLVNYYKAEAVDYQKVLDDTMAVADILTSM
VVDVSDLLDQARQRGDFVMFEGAQGTLLDIDHGTYPYVTSSNTTAGGVAT
GSGLGPRYVDYVLGILKAYSTRVGAGPFPTELFDETGEFLCKQGNEFGAT
TGRRRRTGWLDTVAVRRAVQLNSLSGFCLTKLDVLDGLKEVKLCVAYRMP
DGREVTTTPLAADDWKGVEPIYETMPGWSESTFGVKDRSGLPQAALNYIK
RIEELTGVPIDIISTGPDRTETMILRDPFDA
Ligand information
Ligand IDRPD
InChIInChI=1S/C13H22N3O13P/c17-5-16(24)6(10(20)21)2-1-3-15-11(22)13(14-12(15)23)9(19)8(18)7(29-13)4-28-30(25,26)27/h6-9,17-19,24H,1-5H2,(H,14,23)(H,20,21)(H2,25,26,27)/t6-,7-,8-,9-,13+/m1/s1
InChIKeyMAXSFYCTFIBEAR-OJMIUMIFSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OCN(O)[C@H](CCCN1C(=O)N[C@@]2(O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O)C(O)=O
CACTVS 3.341OCN(O)[CH](CCCN1C(=O)N[C]2(O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C1=O)C(O)=O
OpenEye OEToolkits 1.5.0C(CC(C(=O)O)N(CO)O)CN1C(=O)C2(C(C(C(O2)COP(=O)(O)O)O)O)NC1=O
OpenEye OEToolkits 1.5.0C(C[C@H](C(=O)O)[N@](CO)O)CN1C(=O)[C@@]2([C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)NC1=O
ACDLabs 10.04O=C(O)C(N(O)CO)CCCN2C(=O)C1(OC(C(O)C1O)COP(=O)(O)O)NC2=O
FormulaC13 H22 N3 O13 P
Name(C8-R)-HYDANTOCIDIN 5'-PHOSPHATE;
[8,9-DIHYDROXY-3-(4-CARBOXY-HYDROXY-HYDROXYMETHYL-AMINO-BUTYL)-2,4-DIOXO-6-OXA-1,3-DIAZA-SPIRO[4.4]NON-7-YLMETHYL] PHOSPHATE
ChEMBL
DrugBankDB02666
ZINCZINC000031976939
PDB chain1qf4 Chain A Residue 435 [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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PDB1qf4 An enzyme-bound bisubstrate hybrid inhibitor of adenylosuccinate synthetase
Resolution2.2 Å
Binding residue
(original residue number in PDB)		D13 N38 G40 G127 T128 T129 Q224 L228 V238 V273 G298 A299 T300 T301 R303
Binding residue
(residue number reindexed from 1)		D13 N38 G40 G127 T128 T129 Q224 L228 V238 V273 G298 A299 T300 T301 R303
Annotation score1
Binding affinityMOAD: ic50=0.665uM
PDBbind-CN: -logKd/Ki=6.18,IC50=0.665uM
Enzymatic activity
Catalytic site (original residue number in PDB) D13 K16 G40 H41 Q224
Catalytic site (residue number reindexed from 1) D13 K16 G40 H41 Q224
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:0005515 protein binding
GO:0005525 GTP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding
GO:0097216 guanosine tetraphosphate binding
Biological Process
GO:0006164 purine nucleotide biosynthetic process
GO:0006974 DNA damage response
GO:0015949 nucleobase-containing small molecule interconversion
GO:0044208 'de novo' AMP biosynthetic process
GO:0046040 IMP metabolic process
GO:0046086 adenosine biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane

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Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:1qf4, PDBe:1qf4, PDBj:1qf4
PDBsum1qf4
PubMed10556888
UniProtP0A7D4|PURA_ECOLI Adenylosuccinate synthetase (Gene Name=purA)

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