6XOH

Structure of SUMO1-ML00789344 adduct bound to SAE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.194 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of TAK-981, a First-in-Class Inhibitor of SUMO-Activating Enzyme for the Treatment of Cancer.

Langston, S.P.Grossman, S.England, D.Afroze, R.Bence, N.Bowman, D.Bump, N.Chau, R.Chuang, B.C.Claiborne, C.Cohen, L.Connolly, K.Duffey, M.Durvasula, N.Freeze, S.Gallery, M.Galvin, K.Gaulin, J.Gershman, R.Greenspan, P.Grieves, J.Guo, J.Gulavita, N.Hailu, S.He, X.Hoar, K.Hu, Y.Hu, Z.Ito, M.Kim, M.S.Lane, S.W.Lok, D.Lublinsky, A.Mallender, W.McIntyre, C.Minissale, J.Mizutani, H.Mizutani, M.Molchinova, N.Ono, K.Patil, A.Qian, M.Riceberg, J.Shindi, V.Sintchak, M.D.Song, K.Soucy, T.Wang, Y.Xu, H.Yang, X.Zawadzka, A.Zhang, J.Pulukuri, S.M.

(2021) J Med Chem 64: 2501-2520

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01491
  • Primary Citation of Related Structures:  
    6XOG, 6XOH, 6XOI

  • PubMed Abstract: 

    SUMOylation is a reversible post-translational modification that regulates protein function through covalent attachment of small ubiquitin-like modifier (SUMO) proteins. The process of SUMOylating proteins involves an enzymatic cascade, the first step of which entails the activation of a SUMO protein through an ATP-dependent process catalyzed by SUMO-activating enzyme (SAE). Here, we describe the identification of TAK-981, a mechanism-based inhibitor of SAE which forms a SUMO-TAK-981 adduct as the inhibitory species within the enzyme catalytic site. Optimization of selectivity against related enzymes as well as enhancement of mean residence time of the adduct were critical to the identification of compounds with potent cellular pathway inhibition and ultimately a prolonged pharmacodynamic effect and efficacy in preclinical tumor models, culminating in the identification of the clinical molecule TAK-981.


  • Organizational Affiliation

    Millennium Pharmaceuticals, a wholly owned subsidiary of Takeda Pharmaceuticals Company Ltd., Cambridge, Massachusetts 02139, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SUMO-activating enzyme subunit 1346Homo sapiensMutation(s): 0 
Gene Names: SAE1AOS1SUA1UBLE1A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBE0 (Homo sapiens)
Explore Q9UBE0 
Go to UniProtKB:  Q9UBE0
GTEx:  ENSG00000142230 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBE0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SUMO-activating enzyme subunit 2640Homo sapiensMutation(s): 0 
Gene Names: UBA2SAE2UBLE1BHRIHFB2115
EC: 2.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBT2 (Homo sapiens)
Explore Q9UBT2 
Go to UniProtKB:  Q9UBT2
GTEx:  ENSG00000126261 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBT2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 1101Homo sapiensMutation(s): 0 
Gene Names: SUMO1SMT3CSMT3H3UBL1OK/SW-cl.43
UniProt & NIH Common Fund Data Resources
Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
GTEx:  ENSG00000116030 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63165
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VB7 (Subject of Investigation/LOI)
Query on VB7

Download Ideal Coordinates CCD File 
F [auth C]{(1R,2S,4R)-4-[(5-{4-[(1R)-3,4-dihydro-1H-2-benzopyran-1-yl]thiophene-2-carbonyl}pyrimidin-4-yl)amino]-2-hydroxycyclopentyl}methyl sulfamate
C24 H26 N4 O6 S2
HKKCQZRJLCIYQD-NPDZVAPOSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.133α = 90
b = 72.947β = 92.933
c = 126.586γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description