Structure of PDB 4u0m Chain A Binding Site BS04

Receptor Information
>4u0m Chain A (length=387) Species: 243277 (Vibrio cholerae O1 biovar El Tor str. N16961) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTWNFHQYYTNRNDGLMGKLVLTDEEKNNLKALRKIIRLRTRDVFEEAKG
IAKAVKKSALTFEIIQEKVSTTQIKHLSDSEQREVAKLIYEMDDDARDEF
LGLTPRFWTQGSFQYDTLNRPFQPGQEMDIDDGTYMPMPIFESEPKIGHS
LLILLVDASLKSLVAENHGWKFEAKQTCGRIKIEAEKTHINVPMYAIPKD
EFQKKQIALEANRYELDSENVNLALREGDRKWINSDPKIVEDWFNDSCIR
IGKHLRKVCRFMKAWRDAQWDVGGPSSISLMAATVNILDSVAHDASDLGE
TMKIIAKHLPSEFARGVESPDSTDEKPLFPPSYKHGPREMDIMSKLERLP
EILSSAESADSKSEALKKINMAFGNRVTNSELIVLAK
Ligand information
Ligand IDTLL
InChIInChI=1S/C25H32N8O9/c1-33-14(11-28-20-19(33)22(38)32-25(26)31-20)10-27-13-4-2-12(3-5-13)21(37)30-16(24(41)42)6-8-17(34)29-15(23(39)40)7-9-18(35)36/h2-5,14-16,27H,6-11H2,1H3,(H,29,34)(H,30,37)(H,35,36)(H,39,40)(H,41,42)(H4,26,28,31,32,38)/t14-,15-,16-/m0/s1
InChIKeyVNEFZDDORGCJSD-JYJNAYRXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CN1[C@H](CNC2=C1C(=O)N=C(N2)N)CNc3ccc(cc3)C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O
OpenEye OEToolkits 1.9.2CN1C(CNC2=C1C(=O)N=C(N2)N)CNc3ccc(cc3)C(=O)NC(CCC(=O)NC(CCC(=O)O)C(=O)O)C(=O)O
CACTVS 3.385CN1[C@@H](CNc2ccc(cc2)C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(O)=O)C(O)=O)C(O)=O)CNC3=C1C(=O)N=C(N)N3
ACDLabs 12.01O=C(O)C(NC(=O)CCC(C(=O)O)NC(=O)c1ccc(cc1)NCC2N(C=3C(=O)N=C(NC=3NC2)N)C)CCC(=O)O
CACTVS 3.385CN1[CH](CNc2ccc(cc2)C(=O)N[CH](CCC(=O)N[CH](CCC(O)=O)C(O)=O)C(O)=O)CNC3=C1C(=O)N=C(N)N3
FormulaC25 H32 N8 O9
NameN-[4-({[(6S)-2-amino-5-methyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-gamma-glutamyl-L-glutamic acid
ChEMBL
DrugBank
ZINCZINC000098209452
PDB chain4u0m Chain A Residue 504 [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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PDB4u0m Structural Biochemistry of a Vibrio cholerae Dinucleotide Cyclase Reveals Cyclase Activity Regulation by Folates.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		R36 R40 R108 F109 W110 Y137 F204 E239 L240 D260 K262
Binding residue
(residue number reindexed from 1)		R34 R38 R106 F107 W108 Y135 F202 E215 L216 D236 K238
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.77,IC50=1.69uM
Enzymatic activity
Enzyme Commision number 2.7.7.-
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0005525 GTP binding
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
GO:0052621 diguanylate cyclase activity
GO:0140701 3',3'-cyclic GMP-AMP synthase activity
Biological Process
GO:0009117 nucleotide metabolic process
GO:0009190 cyclic nucleotide biosynthetic process
GO:0050922 negative regulation of chemotaxis
GO:0051607 defense response to virus
Cellular Component
GO:0005575 cellular_component

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4u0m, PDBe:4u0m, PDBj:4u0m
PDBsum4u0m
PubMed25201413
UniProtQ9KVG7|DNCV_VIBCH Cyclic GMP-AMP synthase (Gene Name=dncV)

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