Structure of PDB 5tsd Chain A Binding Site BS01

Receptor Information

>5tsd Chain A (length=316) Species: 347834 (Rhizobium etli CFN 42)

RPPVLVDIKFNPEGVDRVLKTAFADRGSINLADPANRERDFSETEYALLW
KPDADLFRRAPNLKVIFSGGAGVDHIIGMAGLPDIPIVRFVDRSLTTRMS
EWVVMQCLMHLRGQYGHDSHQRRREWAKLIAPEAAEVTVGVMGLGILGQD
AVAKLKVMGFNVIGWSRTRKTIEGVETFDAGELDRFLAKTDILVGLLPLT
PETTGFYDSELFKKLRRDGALGQPVFINAGRGKSQIETDIVSAVREGTLG
GASLDVFEVEPLATDSPLWELENVFITPHDAAVSEENALFRHVEMQIARF
ERGEPLQFVIDRAAGY

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: 5tsd Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5tsd Crystal structure of NADPH-dependent 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADPH and oxalate
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): A74 R92 M102 G146 L147 G148 I149 L150 W168 S169 R170 T171 K173 L200 P201 A232 G233 R234 D258 H282 Y319
• Binding residue (residue number reindexed from 1): A71 R89 M99 G143 L144 G145 I146 L147 W165 S166 R167 T168 K170 L197 P198 A229 G230 R231 D255 H279 Y316
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): E263 H282
• Catalytic site (residue number reindexed from 1): E260 H279

Gene Ontology

Molecular Function

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

External links

• PDB: RCSB:5tsd, PDBe:5tsd, PDBj:5tsd
• PDBsum: 5tsd
• UniProt: Q2KDT2