Structure of PDB 5vg6 Chain D Binding Site BS01

Receptor Information

>5vg6 Chain D (length=308) Species: 78245 (Xanthobacter autotrophicus Py2)

ALVFYSAVDIGQDWKSALQAAHPGLDVRIARAGDGHVEGDPEEVRYALVW
KPPHGFFARFPNLKLVINLGAGVDALVARDDLPDVPVTRLSDPNMSQMMA
SFVLFCVLRHARDIPTFERAQREGRWHYVHPRTAAEIRVGVLGLGDLGAA
AALELARHGFDVRGWSRTEGVSCFHGLEALPGFLAGSEIVVVMLPLTPET
RGLMNAERLAHLPRGAKFINVARGPVVDEAALIAALRSGHIAEATLDVFE
VEPLPVGSPLWAMDNVLVTPHLASIAIPRTAAPQIVENIRRIEAGEPVLN
QVDPRRGY

Ligand information

• Ligand ID: NDP
• InChI: InChI=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
• InChIKey: ACFIXJIJDZMPPO-NNYOXOHSSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(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 3.341: NC(=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 3.341: NC(=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 1.5.0: c1nc(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
• Formula: C21 H30 N7 O17 P3
• Name: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
• ChEMBL: CHEMBL407009
• DrugBank: DB02338
• ZINC: ZINC000008215411
• PDB chain: 5vg6 Chain D Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5vg6 Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2 in complex with NADPH and MES.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): A78 G79 R96 M106 L151 G152 D153 L154 W172 S173 R174 T175 L205 P206 V232 A233 R234 D258 H282 A284 Y319
• Binding residue (residue number reindexed from 1): A71 G72 R89 M99 L144 G145 D146 L147 W165 S166 R167 T168 L194 P195 V221 A222 R223 D247 H271 A273 Y308
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): M102 R234 D258 E263 H282
• Catalytic site (residue number reindexed from 1): M95 R223 D247 E252 H271

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0051287 NAD binding

External links

• PDB: RCSB:5vg6, PDBe:5vg6, PDBj:5vg6
• PDBsum: 5vg6
• UniProt: A7IIH0