Structure of PDB 8vl9 Chain D Binding Site BS01

Receptor Information
>8vl9 Chain D (length=185) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLKPRTLADLIRILHQLFAGDEVNVEEVQAIMEAYESDPTEWAMYAKFDQ
YRYTRNLVDQGNGKFNLMILCWGEGHGSSIHDHTNSHCFLKMLQGNLKET
LFAWPDKKSNEMVKKSERVLRENQCAYINDSIGLHRVENISHTEPAVSLH
LYSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTP
Ligand information
Ligand IDA1ACI
InChIInChI=1S/C27H33N5O4/c1-16(33)30-24(27(2,3)4)26(36)32-15-18(34)13-23(32)25(35)28-14-17-9-10-21(22-11-12-29-31-22)20-8-6-5-7-19(17)20/h5-12,18,23-24,34H,13-15H2,1-4H3,(H,28,35)(H,29,31)(H,30,33)/t18-,23+,24-/m1/s1
InChIKeySURFMMPUSCEGRF-PUZWTLIVSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)N[C@H](C(=O)N1C[C@H](O)C[C@H]1C(=O)NCc2ccc(c3cc[nH]n3)c4ccccc24)C(C)(C)C
CACTVS 3.385CC(=O)N[CH](C(=O)N1C[CH](O)C[CH]1C(=O)NCc2ccc(c3cc[nH]n3)c4ccccc24)C(C)(C)C
OpenEye OEToolkits 2.0.7CC(=O)NC(C(=O)N1CC(CC1C(=O)NCc2ccc(c3c2cccc3)c4cc[nH]n4)O)C(C)(C)C
ACDLabs 12.01CC(C)(C)C(NC(C)=O)C(=O)N1CC(O)CC1C(=O)NCc1ccc(c2cc[NH]n2)c2ccccc12
OpenEye OEToolkits 2.0.7CC(=O)N[C@H](C(=O)N1C[C@@H](C[C@H]1C(=O)NCc2ccc(c3c2cccc3)c4cc[nH]n4)O)C(C)(C)C
FormulaC27 H33 N5 O4
NameN-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[(4P)-4-(1H-pyrazol-3-yl)naphthalen-1-yl]methyl}-L-prolinamide
ChEMBL
DrugBank
ZINC
PDB chain8vl9 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8vl9 A small molecule VHL molecular glue degrader for cysteine dioxygenase 1
Resolution2.5 Å
Binding residue
(original residue number in PDB)		P44 W47 F53 Q99 P150
Binding residue
(residue number reindexed from 1)		P39 W42 F48 Q94 P145
Annotation score1
Enzymatic activity
Enzyme Commision number 1.13.11.20: cysteine dioxygenase.
Gene Ontology
Molecular Function
GO:0005506 iron ion binding
GO:0008198 ferrous iron binding
GO:0008270 zinc ion binding
GO:0016151 nickel cation binding
GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
GO:0017172 cysteine dioxygenase activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
Biological Process
GO:0000097 sulfur amino acid biosynthetic process
GO:0006534 cysteine metabolic process
GO:0006954 inflammatory response
GO:0007595 lactation
GO:0019448 L-cysteine catabolic process
GO:0033762 response to glucagon
GO:0042412 taurine biosynthetic process
GO:0043200 response to amino acid
GO:0045471 response to ethanol
GO:0051384 response to glucocorticoid
GO:0051591 response to cAMP
Cellular Component
GO:0005829 cytosol

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Biological Process
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Cellular Component
External links
PDB RCSB:8vl9, PDBe:8vl9, PDBj:8vl9
PDBsum8vl9
PubMed
UniProtQ16878|CDO1_HUMAN Cysteine dioxygenase type 1 (Gene Name=CDO1)

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