Structure of PDB 1ojd Chain D Binding Site BS01

Receptor Information

>1ojd Chain D (length=494) Species: 9606 (Homo sapiens)

KCDVVVVGGGISGMAAAKLLHDSGLNVVVLEARDRVGGRTYTLRNQKVKY
VDLGGSYVGPTQNRILRLAKELGLETYKVNEVERLIHHVKGKSYPFRGPF
PPVWNPITYLDHNNFWRTMDDMGREIPSDAPWKAPLAEEWDNMTMKELLD
KLCWTESAKQLATLFVNLCVTAETHEVSALWFLWYVKQCGGTTRIISTTN
GGQERKFVGGSGQVSERIMDLLGDRVKLERPVIYIDQTRENVLVETLNHE
MYEAKYVISAIPPTLGMKIHFNPPLPMMRNQMITRVPLGSVIKCIVYYKE
PFWRKKDYCGTMIIDGEEAPVAYTLDDTKPEGNYAAIMGFILAHKARKLA
RLTKEERLKKLCELYAKVLGSLEALEPVHYEEKNWCEEQYSGGCYTTYFP
PGILTQYGRVLRQPVDRIYFAGTETATHWSGYMEGAVEAGERAAREILHA
MGKIPEDEIWQSEPESVDVPAQPITTTFLERHLPSVPGLLRLIG

Ligand information

• Ligand ID: FAD
• InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
  ACDLabs 10.04: O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 1ojd Chain D Residue 600

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1ojd Insights Into the Mode of Inhibition of Human Mitochondrial Monoamine Oxidase B from High-Resolution Crystal Structures
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): G11 G12 G13 S15 E34 A35 R36 G41 R42 G58 S59 Y60 P234 V235 I264 W388 Y393 C397 Y398 G425 T426 G434 Y435 M436 A439
• Binding residue (residue number reindexed from 1): G8 G9 G10 S12 E31 A32 R33 G38 R39 G55 S56 Y57 P231 V232 I261 W385 Y390 C394 Y395 G422 T423 G431 Y432 M433 A436
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): G62 R197 K296
• Catalytic site (residue number reindexed from 1): G59 R194 K293
• Enzyme Commision number: 1.4.3.21: primary-amine oxidase.
  1.4.3.4: monoamine oxidase.

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0008131 primary methylamine oxidase activity
• GO:0009055 electron transfer activity
• GO:0016491 oxidoreductase activity
• GO:0042802 identical protein binding
• GO:0050660 flavin adenine dinucleotide binding
• GO:0052595 aliphatic amine oxidase activity
• GO:0097621 monoamine oxidase activity

Biological Process

• GO:0009410 response to xenobiotic stimulus
• GO:0009636 response to toxic substance
• GO:0010044 response to aluminum ion
• GO:0010269 response to selenium ion
• GO:0014063 negative regulation of serotonin secretion
• GO:0019607 phenylethylamine catabolic process
• GO:0021762 substantia nigra development
• GO:0032496 response to lipopolysaccharide
• GO:0042420 dopamine catabolic process
• GO:0045471 response to ethanol
• GO:0045964 positive regulation of dopamine metabolic process
• GO:0048545 response to steroid hormone
• GO:0050665 hydrogen peroxide biosynthetic process
• GO:0051412 response to corticosterone

Cellular Component

• GO:0005739 mitochondrion
• GO:0005740 mitochondrial envelope
• GO:0005741 mitochondrial outer membrane
• GO:0030425 dendrite
• GO:0043025 neuronal cell body

External links

• PDB: RCSB:1ojd, PDBe:1ojd, PDBj:1ojd
• PDBsum: 1ojd
• PubMed: 12913124
• UniProt: P27338|AOFB_HUMAN Amine oxidase [flavin-containing] B (Gene Name=MAOB)