Structure of PDB 3rhr Chain B Binding Site BS01

Receptor Information

>3rhr Chain B (length=498) Species: 10116 (Rattus norvegicus)

VINYVEKAVNKLTLQMPYQLFIGGEFVDAEGSKTYNTINPTDGSVICQVS
LAQVSDVDKAVAAAKEAFENGLWGKINARDRGRLLYRLADVMEQHQEELA
TIEALDAGAVYTLALKTHVGMSIQTFRYFAGWCDKIQGATIPINQARPNR
NLTLTKKEPVGVCGIVIPWNYPLMMLSWKTAACLAAGNTVVIKPAQVTPL
TALKFAELTLKAGIPKGVVNILPGSGSLVGQRLSDHPDVRKIGFTGSTEV
GKHIMKSCALSNVKKVSLELGGKSPLIIFADCDLNKAVQMGMSSVFFNKG
ENAIAAGRLFVEESIHNQFVQKVVEEVEKMKIGNPLERDTNHGPQNHEAH
LRKLVEYCQRGVKEGATLVCGGNQVPRPGFFFQPTVFTDVEDHMYIAKEE
SFGPIMIISRFADGDVDAVLSRANATEFGLASGVFTRDINKALYVSDKLQ
AGTVFINTYNKTDVAAPFGGFKQSGFGKDLGEAALNEYLRIKTVTFEY

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: 3rhr Chain B Residue 903

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3rhr Conserved catalytic residues of the ALDH1L1 aldehyde dehydrogenase domain control binding and discharging of the coenzyme.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): V570 I571 P572 W573 N574 K597 A599 Q600 S629 G630 G634 Q635 F648 T649 G650 S651 V654 I658 E673 L674 G675 A707 E804 F806 F872
• Binding residue (residue number reindexed from 1): V166 I167 P168 W169 N170 K193 A195 Q196 S225 G226 G230 Q231 F244 T245 G246 S247 V250 I254 E269 L270 G271 A303 E400 F402 F468
• Annotation score: 4
• Binding affinity: MOAD: Kd=5.7uM

Enzymatic activity

• Catalytic site (original residue number in PDB): N574 K597 E673 A707 E804 D883
• Catalytic site (residue number reindexed from 1): N170 K193 E269 A303 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:3rhr, PDBe:3rhr, PDBj:3rhr
• PDBsum: 3rhr
• PubMed: 21540484
• UniProt: P28037|AL1L1_RAT Cytosolic 10-formyltetrahydrofolate dehydrogenase (Gene Name=Aldh1l1)