Structure of PDB 6gh9 Chain A Binding Site BS02

Receptor Information
>6gh9 Chain A (length=331) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPL
GMRGEIAKSYAELIKQMWSGKFSYVTPRAFKTQVGRFAPQQELLAFLLDG
LHEDLNRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGL
FKSTLVCPECAKISVTFDPFCYLTLPLASKVKLKDCIELFTTKEKLGAED
PWYCPNCKEHQQATKKLDLWSLPPVLVVHLKRFSDKLDTLVDFPINDLDM
SEFLINPNAGPCRYNLIAVSNHYGGMGGGHYTAFAKNKDDGKWYYFDDSS
VSTASEDQIVSKAAYVLFYQRQDTFSGTGFF
Ligand information
Ligand IDMIX
InChIInChI=1S/C22H28N4O6/c27-11-9-23-5-7-25-13-1-2-14(26-8-6-24-10-12-28)18-17(13)21(31)19-15(29)3-4-16(30)20(19)22(18)32/h1-4,23-30H,5-12H2
InChIKeyKKZJGLLVHKMTCM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OCCNCCNc1ccc(NCCNCCO)c2C(=O)c3c(O)ccc(O)c3C(=O)c12
ACDLabs 10.04O=C2c1c(c(NCCNCCO)ccc1NCCNCCO)C(=O)c3c2c(O)ccc3O
OpenEye OEToolkits 1.5.0c1cc(c2c(c1NCCNCCO)C(=O)c3c(ccc(c3C2=O)O)O)NCCNCCO
FormulaC22 H28 N4 O6
Name1,4-DIHYDROXY-5,8-BIS({2-[(2-HYDROXYETHYL)AMINO]ETHYL}AMINO)-9,10-ANTHRACENEDIONE;
MITOXANTRONE;
1,4-DIHYDROXY-5,8-BIS({2-[(2-HYDROXYETHYL)AMINO]ETHYL}AMINO)ANTHRA-9,10-QUINONE
ChEMBLCHEMBL58
DrugBankDB01204
ZINCZINC000003794794
PDB chain6gh9 Chain A Residue 1003 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6gh9 The structure of the deubiquitinase USP15 reveals a misaligned catalytic triad and an open ubiquitin-binding channel.
Resolution2.09 Å
Binding residue
(original residue number in PDB)		Y855 G856 H862
Binding residue
(residue number reindexed from 1)		Y273 G274 H280
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.48,IC50=33uM
Enzymatic activity
Enzyme Commision number 3.4.19.12: ubiquitinyl hydrolase 1.
Gene Ontology
Molecular Function
GO:0004843 cysteine-type deubiquitinase activity
Biological Process
GO:0016579 protein deubiquitination

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6gh9, PDBe:6gh9, PDBj:6gh9
PDBsum6gh9
PubMed30228188
UniProtQ9Y4E8|UBP15_HUMAN Ubiquitin carboxyl-terminal hydrolase 15 (Gene Name=USP15)

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