Structure of PDB 3rhj Chain D Binding Site BS01

Receptor Information

>3rhj Chain D (length=498) Species: 10116 (Rattus norvegicus)

VINYVEKAVNKLTLQMPYQLFIGGEFVDAEGSKTYNTINPTDGSVICQVS
LAQVSDVDKAVAAAKEAFENGLWGKINARDRGRLLYRLADVMEQHQEELA
TIEALDAGAVYTLALKTHVGMSIQTFRYFAGWCDKIQGATIPINQARPNR
NLTLTKKEPVGVCGIVIPWNYPLMMLSWKTAACLAAGNTVVIKPAQVTPL
TALKFAELTLKAGIPKGVVNILPGSGSLVGQRLSDHPDVRKIGFTGSTEV
GKHIMKSCALSNVKKVSLALGGKSPLIIFADCDLNKAVQMGMSSVFFNKG
ENCIAAGRLFVEESIHNQFVQKVVEEVEKMKIGNPLERDTNHGPQNHEAH
LRKLVEYCQRGVKEGATLVCGGNQVPRPGFFFQPTVFTDVEDHMYIAKEE
SFGPIMIISRFADGDVDAVLSRANATEFGLASGVFTRDINKALYVSDKLQ
AGTVFINTYNKTDVAAPFGGFKQSGFGKDLGEAALNEYLRIKTVTFEY

Ligand information

• Ligand ID: NAP
• InChI: InChI=1S/C21H28N7O17P3/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/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: XJLXINKUBYWONI-NNYOXOHSSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[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)c1ccc[n+](c1)[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: c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
• Formula: C21 H28 N7 O17 P3
• Name: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
  2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
• ChEMBL: CHEMBL295069
• DrugBank: DB03461
• PDB chain: 3rhj Chain D Residue 101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3rhj Conserved catalytic residues of the ALDH1L1 aldehyde dehydrogenase domain control binding and discharging of the coenzyme.
• Resolution: 1.89 Å
• Binding residue (original residue number in PDB): V570 I571 P572 W573 K597 A599 Q600 S629 G630 G634 Q635 F648 T649 G650 S651 V654 I658 A673 L674 G675 C707 E804 F806 F872
• Binding residue (residue number reindexed from 1): V166 I167 P168 W169 K193 A195 Q196 S225 G226 G230 Q231 F244 T245 G246 S247 V250 I254 A269 L270 G271 C303 E400 F402 F468
• Annotation score: 4
• Binding affinity: MOAD: Kd=0.0073uM

Enzymatic activity

• Catalytic site (original residue number in PDB): N574 K597 A673 C707 E804 D883
• Catalytic site (residue number reindexed from 1): N170 K193 A269 C303 E400 D479
• Enzyme Commision number: 1.5.1.6: formyltetrahydrofolate dehydrogenase.

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity
• GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor

External links

• PDB: RCSB:3rhj, PDBe:3rhj, PDBj:3rhj
• PDBsum: 3rhj
• PubMed: 21540484
• UniProt: P28037|AL1L1_RAT Cytosolic 10-formyltetrahydrofolate dehydrogenase (Gene Name=Aldh1l1)