6XOG

Structure of SUMO1-ML786519 adduct bound to SAE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 

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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) ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUMO-activating enzyme subunit 1A346Homo sapiensMutation(s): 0 
Gene Names: SAE1, AOS1, SUA1, UBLE1A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBE0 (Homo sapiens)
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Go to UniProtKB:  Q9UBE0
PHAROS:  Q9UBE0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBE0
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SUMO-activating enzyme subunit 2B640Homo sapiensMutation(s): 0 
Gene Names: UBA2, SAE2, UBLE1B, HRIHFB2115
EC: 2.3.2
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Find proteins for Q9UBT2 (Homo sapiens)
Explore Q9UBT2 
Go to UniProtKB:  Q9UBT2
PHAROS:  Q9UBT2
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UniProt GroupQ9UBT2
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 1C101Homo sapiensMutation(s): 0 
Gene Names: SUMO1, SMT3C, SMT3H3, UBL1, OK/SW-cl.43
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Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
PHAROS:  P63165
Entity Groups  
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UniProt GroupP63165
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VAY (Subject of Investigation/LOI)
Query on VAY
Download Ideal Coordinates CCD File 
F [auth C]{(1R,2R,3S,4R)-4-[(5-{4-[(1S)-1-(6-bromopyridin-2-yl)-1-hydroxyethyl]thiophene-2-carbonyl}pyrimidin-4-yl)amino]-2,3-dihydroxycyclopentyl}methyl sulfamate
C22 H24 Br N5 O7 S2
IZYVMHSGDZFGFW-SULQKKJVSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.9α = 90
b = 72.422β = 93.858
c = 126.87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references