Structure of PDB 5gz6 Chain A Binding Site BS01

Receptor Information
>5gz6 Chain A (length=318) Species: 51173 (Ureibacillus thermosphaericus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKIRIGIVGYGNLGRGVEAAIQQNPDMELVAVFTRRDPKTVAVKSNVKVL
HVDDAQSYKDEIDVMILCGGSATDLPEQGPYFAQYFNTIDSFATHARIPD
YFDAVNAAAEQSGKVAIISVGWDPGLFSLNRLLGEVVLPVGNTYTFWGKG
VSLGGAIRRIQGVKNAVQYIIPIDEAVNRVRSGENPELSTREKHAMECFV
VLEEGADPAKVEHEIKTMPNFFDEYDTTVHFISEEELKQNHSGMPNGGFV
IRSGKKQIIEFSLNLESNPMFTSSALVAYARAAYRLSQNGDKGAKTVFDI
PFGLLSPKSPEDLRKELL
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 chain5gz6 Chain A Residue 1001 [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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PDB5gz6 Structure-Based Engineering of an Artificially Generated NADP+-Dependent d-Amino Acid Dehydrogenase
Resolution1.74 Å
Binding residue
(original residue number in PDB)		G10 Y11 G12 N13 L14 T35 R36 R37 G70 G71 S72 S92 A94 G122 W123 D124 P125 T280
Binding residue
(residue number reindexed from 1)		G9 Y10 G11 N12 L13 T34 R35 R36 G69 G70 S71 S91 A93 G121 W122 D123 P124 T272
Annotation score4
Enzymatic activity
Enzyme Commision number 1.4.1.16: diaminopimelate dehydrogenase.
Gene Ontology
Molecular Function
GO:0008839 4-hydroxy-tetrahydrodipicolinate reductase
GO:0016491 oxidoreductase activity
GO:0047850 diaminopimelate dehydrogenase activity
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5gz6, PDBe:5gz6, PDBj:5gz6
PDBsum5gz6
PubMed28363957
UniProtG1UII1|DAPDH_URETH Meso-diaminopimelate D-dehydrogenase (Gene Name=ddh)

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