Structure of PDB 6rkf Chain F Binding Site BS01

Receptor Information
>6rkf Chain F (length=333) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TARIAVVGAGVVGLSTAVCISKLVPRCSVTIISDKFTPDTTSDVAAGMLI
PHTYPDTPIHTQKQWFRETFNHLFAIANSAEAGDAGVHLVSGWQIFQSTP
TEEVPFWADVVLGFRKMTEAELKKFPQYVFGQAFTTLKYEGPAYLPWLEK
RIKGSGGWTLTRRIEDLWELHPSFDIVVNCSGLGSRQLAGDSKIFPVRGQ
VLQVQAPWVEHFIRDGSGLTYIYPGTSHVTLGGTRQKGDWNLSPDAENSR
EILSRCCALEPSLHGACNIREKVGLRPYRPGVRLQTELLARDGQRLPVVH
HYGHGSGGISVHWGTALEAARLVSECVHALRTP
Ligand information
Ligand IDFAD
InChIInChI=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
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=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 1.5.0Cc1cc2c(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 1.5.0Cc1cc2c(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 3.341Cc1cc2N=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 10.04O=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
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain6rkf Chain F Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6rkf Structure and kinetic properties of human d-aspartate oxidase, the enzyme-controlling d-aspartate levels in brain.
Resolution3.219 Å
Binding residue
(original residue number in PDB)		G12 V14 S35 D36 K37 T42 T43 S44 A47 M50 I166 S183 G186 G276 R278 G307 S308 G309 G310 I311 S312
Binding residue
(residue number reindexed from 1)		G10 V12 S33 D34 K35 T40 T41 S42 A45 M48 I164 S181 G184 G274 R276 G305 S306 G307 G308 I309 S310
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) M50 S308 S312
Catalytic site (residue number reindexed from 1) M48 S306 S310
Enzyme Commision number 1.4.3.1: D-aspartate oxidase.
Gene Ontology
Molecular Function
GO:0003884 D-amino-acid oxidase activity
GO:0005515 protein binding
GO:0008445 D-aspartate oxidase activity
GO:0016491 oxidoreductase activity
GO:0047821 D-glutamate oxidase activity
GO:0071949 FAD binding
Biological Process
GO:0006531 aspartate metabolic process
GO:0006533 aspartate catabolic process
GO:0007320 insemination
GO:0007625 grooming behavior
GO:0010646 regulation of cell communication
GO:0019478 D-amino acid catabolic process
GO:0042445 hormone metabolic process
GO:0046416 D-amino acid metabolic process
GO:0050877 nervous system process
Cellular Component
GO:0005737 cytoplasm
GO:0005777 peroxisome
GO:0005782 peroxisomal matrix
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6rkf, PDBe:6rkf, PDBj:6rkf
PDBsum6rkf
PubMed31914658
UniProtQ99489|OXDD_HUMAN D-aspartate oxidase (Gene Name=DDO)

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