6X9K

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3685032A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia.

Pappalardi, M.B.Keenan, K.Cockerill, M.Kellner, W.A.Stowell, A.Sherk, C.Wong, K.Pathuri, S.Briand, J.Steidel, M.Chapman, P.Groy, A.Wiseman, A.K.McHugh, C.F.Campobasso, N.Graves, A.P.Fairweather, E.Werner, T.Raoof, A.Butlin, R.J.Rueda, L.Horton, J.R.Fosbenner, D.T.Zhang, C.Handler, J.L.Muliaditan, M.Mebrahtu, M.Jaworski, J.P.McNulty, D.E.Burt, C.Eberl, H.C.Taylor, A.N.Ho, T.Merrihew, S.Foley, S.W.Rutkowska, A.Li, M.Romeril, S.P.Goldberg, K.Zhang, X.Kershaw, C.S.Bantscheff, M.Jurewicz, A.J.Minthorn, E.Grandi, P.Patel, M.Benowitz, A.B.Mohammad, H.P.Gilmartin, A.G.Prinjha, R.K.Ogilvie, D.Carpenter, C.Heerding, D.Baylin, S.B.Jones, P.A.Cheng, X.King, B.W.Luengo, J.I.Jordan, A.M.Waddell, I.Kruger, R.G.McCabe, M.T.

(2021) Nat Cancer 2: 1002-1017

  • DOI: https://doi.org/10.3324/haematol.2020.248658
  • Primary Citation of Related Structures:  
    6X9I, 6X9J, 6X9K

  • PubMed Abstract: 

    DNA methylation, a key epigenetic driver of transcriptional silencing, is universally dysregulated in cancer. Reversal of DNA methylation by hypomethylating agents, such as the cytidine analogs decitabine or azacytidine, has demonstrated clinical benefit in hematologic malignancies. These nucleoside analogs are incorporated into replicating DNA where they inhibit DNA cytosine methyltransferases DNMT1, DNMT3A and DNMT3B through irreversible covalent interactions. These agents induce notable toxicity to normal blood cells thus limiting their clinical doses. Herein we report the discovery of GSK3685032, a potent first-in-class DNMT1-selective inhibitor that was shown via crystallographic studies to compete with the active-site loop of DNMT1 for penetration into hemi-methylated DNA between two CpG base pairs. GSK3685032 induces robust loss of DNA methylation, transcriptional activation and cancer cell growth inhibition in vitro. Due to improved in vivo tolerability compared with decitabine, GSK3685032 yields superior tumor regression and survival mouse models of acute myeloid leukemia.


  • Organizational Affiliation

    Cancer Epigenetics Research Unit, Oncology, GlaxoSmithKline, Collegeville, PA, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 1874Homo sapiensMutation(s): 0 
Gene Names: DNMT1AIMCXXC9DNMT
EC: 2.1.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for P26358 (Homo sapiens)
Explore P26358 
Go to UniProtKB:  P26358
PHAROS:  P26358
GTEx:  ENSG00000130816 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26358
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*AP*GP*GP*CP*(5CM)P*GP*CP*CP*TP*GP*C)-3')B [auth C]12Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*AP*GP*G)-R(P*(PYO))-D(P*GP*GP*CP*CP*TP*C)-3')C [auth D]12Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UXM (Subject of Investigation/LOI)
Query on UXM

Download Ideal Coordinates CCD File 
O [auth C](2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-phenylacetamide
C22 H24 N6 O S
KNKHRZYILDZLRE-LJQANCHMSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.318α = 90
b = 78.336β = 125.761
c = 117.068γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM134744

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2022-01-19
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description