Structure of PDB 1mc5 Chain B Binding Site BS03

Receptor Information

>1mc5 Chain B (length=373) Species: 9606 (Homo sapiens)

ANEVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDAYT
LSGADPEGCFPVILGHEGAGIVESVGEGVTKLKAGDTVIPLYIPQCGECK
FCLNPKTNLCQKIRVTQGKGLMPDGTSRFTCKGKTILHYMGTSTFSEYTV
VADISVAKIDPLAPLDKVCLLGCGISTGYGAAVNTAKLEPGSVCAVFGLG
GVGLAVIMGCKVAGASRIIGVDINKDKFARAKEFGATECINPQDFSKPIQ
EVLIEMTDGGVDYSFECIGNVKVMRAALEACHKGWGVSVVVGVAASGEEI
ATRPFQLVTGRTWKGTAFGGWKSVESVPKLVSEYMSKKIKVDEFVTHNLS
FDEINKAFELMHSGKSIRTVVKI

Ligand information

• Ligand ID: NAD
• InChI: InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: BAWFJGJZGIEFAR-NNYOXOHSSA-N
• SMILES:
  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)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)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)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]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)O)O)O)O)C(=O)N
• Formula: C21 H27 N7 O14 P2
• Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
• ChEMBL: CHEMBL1234613
• DrugBank: DB14128
• PDB chain: 1mc5 Chain B Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1mc5 Human glutathione-dependent formaldehyde dehydrogenase. Structural changes associated with Ternary Complex formation
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): H45 T177 G198 G200 V202 D222 I223 C267 I268 V291 G292 V293 F318
• Binding residue (residue number reindexed from 1): H45 T177 G198 G200 V202 D222 I223 C267 I268 V291 G292 V293 F318
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): C44 H45 T46 Y49 H66 E67 C96 C99 C102 C110 R114 C173 T177 R368
• Catalytic site (residue number reindexed from 1): C44 H45 T46 Y49 H66 E67 C96 C99 C102 C110 R114 C173 T177 R368
• Enzyme Commision number: 1.1.1.-
  1.1.1.1: alcohol dehydrogenase.
  1.1.1.284: S-(hydroxymethyl)glutathione dehydrogenase.

Gene Ontology

Molecular Function

• GO:0004022 alcohol dehydrogenase (NAD+) activity
• GO:0005504 fatty acid binding
• GO:0008270 zinc ion binding
• GO:0009055 electron transfer activity
• GO:0016491 oxidoreductase activity
• GO:0018467 formaldehyde dehydrogenase (NAD+) activity
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding
• GO:0051903 S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity
• GO:0080007 S-nitrosoglutathione reductase (NADH) activity
• GO:0106321 S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity
• GO:0106322 S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity

Biological Process

• GO:0001523 retinoid metabolic process
• GO:0003016 respiratory system process
• GO:0006629 lipid metabolic process
• GO:0010430 fatty acid omega-oxidation
• GO:0032496 response to lipopolysaccharide
• GO:0044281 small molecule metabolic process
• GO:0045777 positive regulation of blood pressure
• GO:0046294 formaldehyde catabolic process
• GO:0051409 response to nitrosative stress
• GO:0051775 response to redox state

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005829 cytosol
• GO:0070062 extracellular exosome

External links

• PDB: RCSB:1mc5, PDBe:1mc5, PDBj:1mc5
• PDBsum: 1mc5
• PubMed: 12484756
• UniProt: P11766|ADHX_HUMAN Alcohol dehydrogenase class-3 (Gene Name=ADH5)