Structure of PDB 6h3d Chain A Binding Site BS01

Receptor Information
>6h3d Chain A (length=428) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKLLMIGTGPVAIQLANICYLKSDYEIDMVGRASTSEKSKRLYQAYKKEK
QFEVKIQNEAHQHLEGKFEINRLYKDVKNVKGEYETVVMACTADAYYDTL
QQLSLETLQSVKHVILISPTFGSQMIVEQFMSKFSQDIEVISFSTYLGDT
RIVDKEAPNHVLTTGVKKKLYMGSTHSNSTMCQRISALAEQLKIQLEVVE
SPLHAETRNSSLYVHPPLFMNDFSLKAIFEGTDVPVYVYKLFPEGPITMT
LIREMRLMWKEMMAILQAFRVPSVNLLQFMVKENYPVRPETLDEGDIEHF
EILPDILQEYLLYVRYTAILIDPFSQPDENGHYFDFSAVPFKQVYKNEQD
VVQIPRMPSEDYYRTAMIQHIGKMLGIKTPMIDQFLTRYEASCQAYKDMH
QDQQLSSQFNTNLFEGDKALVTKFLEIN
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 chain6h3d Chain A Residue 600 [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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PDB6h3d Control by Metals of Staphylopine Dehydrogenase Activity during Metallophore Biosynthesis.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		G10 P11 V12 R33 S37 K39 S40 C92 T93 T100 S119 D150 T151 R357
Binding residue
(residue number reindexed from 1)		G9 P10 V11 R32 S36 K38 S39 C91 T92 T99 S118 D149 T150 R356
Annotation score4
Enzymatic activity
Enzyme Commision number 1.5.1.52: staphylopine dehydrogenase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity

View graph for
Molecular Function
External links
PDB RCSB:6h3d, PDBe:6h3d, PDBj:6h3d
PDBsum6h3d
PubMed30901200
UniProtA0A0H3JT80|ODH_STAAM Staphylopine synthase (Gene Name=cntM)

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