Structure of PDB 5cpm Chain B Binding Site BS02

Receptor Information

>5cpm Chain B (length=359) Species: 303 (Pseudomonas putida)

SALFEPYTLKDVTLRNRIAIPPMCQYMAEDGLINDWHQVHYASMARGGAG
LLVVEATAVAPEGRITPGCAGIWSDAHAQAFVPVVQAIKAAGSVPGIQIA
HAGRKASANRPWEGDDHIGADDARGWETIAPSAIAFGAHLPNVPRAMTLD
DIARVKQDFVDAARRARDAGFEWIELHFAHGYLGQSFFSEHSNKRTDAYG
GSFDNRSRFLLETLAAVREVWPENLPLTARFGVLEYDGRDEQTLEESIEL
ARRFKAGGLDLLSVSVGFTIPETNIPWGPAFMGPIAERVRREAKLPVTSA
WGFGTPQLAEAALQANQLDLVSVGRAHLADPHWAYFAAKELGVEKASWTL
PAPYAHWLE

Ligand information

• Ligand ID: FNR
• InChI: InChI=1S/C17H23N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,18,22-24H,5-6H2,1-2H3,(H2,27,28,29)(H2,19,20,25,26)/t11-,12+,14-/m0/s1
• InChIKey: YTNIXZGTHTVJBW-SCRDCRAPSA-N
• SMILES:
  CACTVS 3.385: Cc1cc2NC3=C(NC(=O)NC3=O)N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)CC(C(C(COP(=O)(O)O)O)O)O
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
  CACTVS 3.385: Cc1cc2NC3=C(NC(=O)NC3=O)N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
  ACDLabs 12.01: c23N(C=1NC(=O)NC(=O)C=1Nc2cc(C)c(C)c3)CC(O)C(O)C(O)COP(O)(=O)O
• Formula: C17 H23 N4 O9 P
• Name: 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL;
  TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE
• PDB chain: 5cpm Chain B Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5cpm Better than Nature: Nicotinamide Biomimetics That Outperform Natural Coenzymes.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): P22 P23 M24 C25 A57 Q99 H178 H181 R231 A301 W302 G325 R326
• Binding residue (residue number reindexed from 1): P21 P22 M23 C24 A56 Q98 H177 H180 R230 A300 W301 G324 R325
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): C25 H178 H181 Y183 R231 R240
• Catalytic site (residue number reindexed from 1): C24 H177 H180 Y182 R230 R239

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003959 NADPH dehydrogenase activity
• GO:0010181 FMN binding
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0050661 NADP binding

External links

• PDB: RCSB:5cpm, PDBe:5cpm, PDBj:5cpm
• PDBsum: 5cpm
• PubMed: 26727612
• UniProt: Q9R9V9