Structure of PDB 4mdz Chain B Binding Site BS02

Receptor Information
>4mdz Chain B (length=363) Species: 123214 (Persephonella marina EX-H1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YQDPERKLKILLDYSSKIANEKDLRNVLLFLTDLAKEIMEADRASIFLYD
DQKKTLWTIVAHGVDRIEIDADKGIAGYVFRTGEILNIPDAYKDPRFDRD
IDKRTGYRTRTILAVPLFDRKQNIIGVFQVINKLTNSVFTEEDIELLRHI
SLYASSTIENAILYEKLKKAHEDVIYRLSHATKFKDPETQNHIIRVGLYA
EILAREAGLDEEDVELVKLAAPMHDIGKVGIPDRVLLKPGKLNDEEWEIM
KKHTIYGYEILKGGDSRLLQIAADIAIEHHERWDGTGYPFGKKGEEISIY
GRMTSISDVFDALTSDRPYKKAWDMDRTVRFFKEQKGKHFDPFLTDIFLK
NIDQMFSIKRELR
Ligand information
Ligand IDC2E
InChIInChI=1S/C20H24N10O14P2/c21-19-25-13-7(15(33)27-19)23-3-29(13)17-9(31)11-5(41-17)1-39-45(35,36)44-12-6(2-40-46(37,38)43-11)42-18(10(12)32)30-4-24-8-14(30)26-20(22)28-16(8)34/h3-6,9-12,17-18,31-32H,1-2H2,(H,35,36)(H,37,38)(H3,21,25,27,33)(H3,22,26,28,34)/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1
InChIKeyPKFDLKSEZWEFGL-MHARETSRSA-N
SMILES
SoftwareSMILES
ACDLabs 11.02O=C7NC(=Nc1c7ncn1C6OC5COP(=O)(OC4C(OC(n2c3N=C(N)NC(=O)c3nc2)C4O)COP(=O)(O)OC5C6O)O)N
OpenEye OEToolkits 1.7.0c1nc2c(n1C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)n6cnc7c6N=C(NC7=O)N)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.7.0c1nc2c(n1[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@@](=O)(O[C@@H]5[C@@H](CO[P@@](=O)(O4)O)O[C@H]([C@@H]5O)n6cnc7c6N=C(NC7=O)N)O)O)N=C(NC2=O)N
CACTVS 3.352NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO[P](O)(=O)O[CH]4[CH]3O)n6cnc7C(=O)NC(=Nc67)N
CACTVS 3.352NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@H]5[C@@H](O)[C@@H](O[C@@H]5CO[P](O)(=O)O[C@H]4[C@H]3O)n6cnc7C(=O)NC(=Nc67)N
FormulaC20 H24 N10 O14 P2
Name9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one);
c-di-GMP;
Cyclic diguanosine monophosphate
ChEMBLCHEMBL1231573
DrugBank
ZINCZINC000072319544
PDB chain4mdz Chain B Residue 402 [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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PDB4mdz Crystal structure of an HD-GYP domain cyclic-di-GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre.
Resolution2.68 Å
Binding residue
(original residue number in PDB)
G237 L239 W244 H277 Y285 A309 L310 R314
Binding residue
(residue number reindexed from 1)
G240 L242 W247 H280 Y288 A312 L313 R317
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:4mdz, PDBe:4mdz, PDBj:4mdz
PDBsum4mdz
PubMed24176013
UniProtC0QQ26

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