Structure of PDB 5z2l Chain A Binding Site BS01

Receptor Information
>5z2l Chain A (length=239) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GAFTGKTVLILGGSRGIGAAIVRRFVTDGANVRFTYAGSKDAAKRLAQET
GATAVFTDSADRDAVIDVVRKSGALDILVVNAGIGVFGEALELNADDIDR
LFKINIHAPYHASVEAARQMPEGGRILIIGSVNGDRMPVAGMAAYAASKS
ALQGMARGLARDFGPRGITINVVQPGPIDTDANPANGPMRDMLHSLMAIK
RHGQPEEVAGMVAWLAGPEASFVTGAMHTIDGAFGALEH
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain5z2l Chain A Residue 302 [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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PDB5z2l A potential substrate binding pocket of BdcA plays a critical role in NADPH recognition and biofilm dispersal
Resolution1.7 Å
Binding residue
(original residue number in PDB)		S15 R16 I18 Y37 A38 G39 S40 T58 D59 S60 N82 A83 S132 Y146 K150 I179 T181 N184
Binding residue
(residue number reindexed from 1)		S14 R15 I17 Y36 A37 G38 S39 T57 D58 S59 N81 A82 S131 Y145 K149 I178 T180 N183
Annotation score4
Binding affinityMOAD: Kd=45uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0035438 cyclic-di-GMP binding
GO:0042803 protein homodimerization activity
GO:0070402 NADPH binding
Biological Process
GO:0044010 single-species biofilm formation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5z2l, PDBe:5z2l, PDBj:5z2l
PDBsum5z2l
PubMed29462616
UniProtP39333|BDCA_ECOLI Cyclic-di-GMP-binding biofilm dispersal mediator protein (Gene Name=bdcA)

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