Structure of PDB 2du8 Chain B Binding Site BS01

Receptor Information

>2du8 Chain B (length=340) Species: 9606 (Homo sapiens)

MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAG
LWQPYLSDPNNPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHE
AIPDPSWKDTVLGFRKLTPRELDMFPDYGYGWFHTSLILEGKNYLQWLTE
RLTERGVKFFQRKVESFEEVAREGADVIVNCTGVWAGALQRDPLLQPGRG
QIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQTVTLGGIFQLGNWSEL
NNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPVRPQIRLEREQLRTGP
SNTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEEKKLS

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: 2du8 Chain B Residue 1351

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2du8 Crystal structure of human D-amino acid oxidase: Context-dependent variability of the backbone conformation of the VAAGL hydrophobic stretch located at the si-face of the flavin ring
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): G1007 A1008 G1009 V1010 I1011 A1036 D1037 R1038 T1044 T1045 A1048 G1050 L1051 K1163 V1164 T1182 G1281 R1283 G1312 G1313 Y1314 G1315 L1316 T1317
• Binding residue (residue number reindexed from 1): G7 A8 G9 V10 I11 A36 D37 R38 T44 T45 A48 G50 L51 K163 V164 T182 G281 R283 G312 G313 Y314 G315 L316 T317
• Annotation score: 1
• Binding affinity: MOAD: Kd=8uM

Enzymatic activity

• Catalytic site (original residue number in PDB): G1313 T1317
• Catalytic site (residue number reindexed from 1): G313 T317
• Enzyme Commision number: 1.4.3.3: D-amino-acid oxidase.

Gene Ontology

Molecular Function

• GO:0003884 D-amino-acid oxidase activity
• GO:0005515 protein binding
• GO:0016491 oxidoreductase activity
• GO:0042802 identical protein binding
• GO:0071949 FAD binding

Biological Process

• GO:0006562 proline catabolic process
• GO:0007586 digestion
• GO:0019478 D-amino acid catabolic process
• GO:0036088 D-serine catabolic process
• GO:0042416 dopamine biosynthetic process
• GO:0046416 D-amino acid metabolic process
• GO:0055130 D-alanine catabolic process
• GO:0070178 D-serine metabolic process
• GO:0070945 neutrophil-mediated killing of gram-negative bacterium

Cellular Component

• GO:0005576 extracellular region
• GO:0005737 cytoplasm
• GO:0005741 mitochondrial outer membrane
• GO:0005777 peroxisome
• GO:0005782 peroxisomal matrix
• GO:0005829 cytosol
• GO:0042995 cell projection
• GO:0045202 synapse
• GO:0048786 presynaptic active zone

External links

• PDB: RCSB:2du8, PDBe:2du8, PDBj:2du8
• PDBsum: 2du8
• PubMed: 17088322
• UniProt: P14920|OXDA_HUMAN D-amino-acid oxidase (Gene Name=DAO)