7SFC

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3735967A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors.

Horton, J.R.Pathuri, S.Wong, K.Ren, R.Rueda, L.Fosbenner, D.T.Heerding, D.A.McCabe, M.T.Pappalardi, M.B.Zhang, X.King, B.W.Cheng, X.

(2022) Structure 30: 793-802.e5

  • DOI: 10.1016/j.str.2022.03.009
  • Primary Citation of Related Structures:  
    7SFC, 7SFD, 7SFE, 7SFF, 7SFG

  • PubMed Abstract: 
  • DNMT1 maintains the parental DNA methylation pattern on newly replicated hemimethylated DNA. The failure of this maintenance process causes aberrant DNA methylation that affects transcription and contributes to the development and progression of cancers such as acute myeloid leukemia ...

    DNMT1 maintains the parental DNA methylation pattern on newly replicated hemimethylated DNA. The failure of this maintenance process causes aberrant DNA methylation that affects transcription and contributes to the development and progression of cancers such as acute myeloid leukemia. Here, we structurally characterized a set of newly discovered DNMT1-selective, reversible, non-nucleoside inhibitors that bear a core 3,5-dicyanopyridine moiety, as exemplified by GSK3735967, to better understand their mechanism of inhibition. All of the dicyanopydridine-containing inhibitors examined intercalate into the hemimethylated DNA between two CpG base pairs through the DNA minor groove, resulting in conformational movement of the DNMT1 active-site loop. In addition, GSK3735967 introduces two new binding sites, where it interacts with and stabilizes the displaced DNMT1 active-site loop and it occupies an open aromatic cage in which trimethylated histone H4 lysine 20 is expected to bind. Our work represents a substantial step in generating potent, selective, and non-nucleoside inhibitors of DNMT1.


    Organizational Affiliation

    Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: xcheng5@mdanderson.org.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase 1A874Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26358
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (12-MER)B [auth C]12Homo sapiens
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (12-MER)C [auth D]12Homo sapiens
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I67 (Subject of Investigation/LOI)
Query on I67

Download Ideal Coordinates CCD File 
BA [auth C],
F [auth A],
G [auth A]
N-{[4-({[3,5-dicyano-4-ethyl-6-(4-methyl-1,4-diazepan-1-yl)pyridin-2-yl]sulfanyl}methyl)phenyl]methyl}glycinamide
C25 H31 N7 O S
QPLFMVVUDGWTPG-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
N [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
AA [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
AA [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.733α = 90
b = 78.897β = 125.644
c = 117.335γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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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: 2022-03-30
    Type: Initial release
  • Version 1.1: 2022-04-20
    Changes: Database references
  • Version 1.2: 2022-06-15
    Changes: Database references