3GZN

Structure of NEDD8-activating enzyme in complex with NEDD8 and MLN4924


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Substrate-assisted inhibition of ubiquitin-like protein-activating enzymes: the NEDD8 E1 inhibitor MLN4924 forms a NEDD8-AMP mimetic in situ.

Brownell, J.E.Sintchak, M.D.Gavin, J.M.Liao, H.Bruzzese, F.J.Bump, N.J.Soucy, T.A.Milhollen, M.A.Yang, X.Burkhardt, A.L.Ma, J.Loke, H.K.Lingaraj, T.Wu, D.Hamman, K.B.Spelman, J.J.Cullis, C.A.Langston, S.P.Vyskocil, S.Sells, T.B.Mallender, W.D.Visiers, I.Li, P.Claiborne, C.F.Rolfe, M.Bolen, J.B.Dick, L.R.

(2010) Mol Cell 37: 102-111

  • DOI: https://doi.org/10.1016/j.molcel.2009.12.024
  • Primary Citation of Related Structures:  
    3GZN

  • PubMed Abstract: 

    The NEDD8-activating enzyme (NAE) initiates a protein homeostatic pathway essential for cancer cell growth and survival. MLN4924 is a selective inhibitor of NAE currently in clinical trials for the treatment of cancer. Here, we show that MLN4924 is a mechanism-based inhibitor of NAE and creates a covalent NEDD8-MLN4924 adduct catalyzed by the enzyme. The NEDD8-MLN4924 adduct resembles NEDD8 adenylate, the first intermediate in the NAE reaction cycle, but cannot be further utilized in subsequent intraenzyme reactions. The stability of the NEDD8-MLN4924 adduct within the NAE active site blocks enzyme activity, thereby accounting for the potent inhibition of the NEDD8 pathway by MLN4924. Importantly, we have determined that compounds resembling MLN4924 demonstrate the ability to form analogous adducts with other ubiquitin-like proteins (UBLs) catalyzed by their cognate-activating enzymes. These findings reveal insights into the mechanism of E1s and suggest a general strategy for selective inhibition of UBL conjugation pathways.


  • Organizational Affiliation

    Discovery, Millennium Pharmaceuticals, Inc., 40 Landsdowne Street, Cambridge, MA 02139, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NEDD8-activating enzyme E1 regulatory subunit
A, C
534Homo sapiensMutation(s): 0 
Gene Names: APPBP1HPP1NAE1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13564 (Homo sapiens)
Explore Q13564 
Go to UniProtKB:  Q13564
PHAROS:  Q13564
GTEx:  ENSG00000159593 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13564
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NEDD8-activating enzyme E1 catalytic subunit
B, D
463Homo sapiensMutation(s): 0 
Gene Names: UBA3UBE1C
EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TBC4 (Homo sapiens)
Explore Q8TBC4 
Go to UniProtKB:  Q8TBC4
PHAROS:  Q8TBC4
GTEx:  ENSG00000144744 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TBC4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NEDD8E [auth I],
F [auth J]
82Homo sapiensMutation(s): 0 
Gene Names: NEDD8
UniProt & NIH Common Fund Data Resources
Find proteins for Q15843 (Homo sapiens)
Explore Q15843 
Go to UniProtKB:  Q15843
PHAROS:  Q15843
GTEx:  ENSG00000129559 
Entity Groups  
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UniProt GroupQ15843
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B39
Query on B39

Download Ideal Coordinates CCD File 
I, J
[(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate
C21 H25 N5 O4 S
MPUQHZXIXSTTDU-QXGSTGNESA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth B],
H [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
B39 PDBBind:  3GZN IC50: 10 (nM) from 1 assay(s)
BindingDB:  3GZN IC50: min: 4.7, max: 180 (nM) from 3 assay(s)
EC50: 3400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.233 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.03α = 90
b = 228.715β = 90
c = 229.307γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description