Structure of PDB 3gfx Chain A Binding Site BS02

Receptor Information
>3gfx Chain A (length=392) Species: 272620 (Klebsiella pneumoniae subsp. pneumoniae MGH 78578) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLTTLIYRSQVHPDRPPVDLDALVHRASSKNLPLGITGILLFNGLQFFQV
LEGTEEALESLFSEIQSDPRHRDVVELMRDYSAYRRFHGTGMRILDLRLF
ETDGALEEILRFSTPVNDRMFRLLSAFIADGGRYCLPEPLQPSRWMMMPA
TAAPQHLPGQPCQFALQAIVEPAKKRVSSFEALIRSPTGGSPVEMFAAIA
AEDRYRFDLESKAYAFALAGQLPLGKHQLAINLLPGSLYHHPDAVGWLMD
SLLAAGLRPDQVLIEVTETEVITCFDQFRKVLKALRVAGMKLAIDDFGAG
YSGLSLLTRFQPDKIKVDAELVRDIHISGTKQAIVASVVRCCEDLGITVV
AEGVETLEEWCWLQSVGIRLFQGFLFSRPCLNGIGEICWPVA
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 chain3gfx 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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PDB3gfx Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)
Q174 L190 I191 R192 P199 D215 K219 N239 D302 G360 E362 G380 F381
Binding residue
(residue number reindexed from 1)
Q167 L183 I184 R185 P192 D208 K212 N232 D295 G353 E355 G373 F374
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0009882 blue light photoreceptor activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0071949 FAD binding
Biological Process
GO:0009785 blue light signaling pathway

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:3gfx, PDBe:3gfx, PDBj:3gfx
PDBsum3gfx
PubMed19536266
UniProtA6T8V8

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