Macromolecule Content

Total Structure Weight: 48479.27
Atom Count: 2771
Residue Count: 421
Unique protein chains: 1

4EQZ

Crystal structure of human DOT1L in complex with inhibitor FED2

DOI: 10.2210/pdb4EQZ/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli

Deposited: 2012-04-19 Released: 2012-05-02
Deposition Author(s): Wernimont, A.K., Tempel, W., Yu, W., Li, Y., Nguyen, K.T., Federation, A., Marineau, J., Qi, J., Vedadi, M., Bradner, J.E., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Brown, P.J., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.221
R-Value Work: 0.199

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Catalytic site remodelling of the DOT1L methyltransferase by selective inhibitors.

Yu, W., Chory, E.J., Wernimont, A.K., Tempel, W., Scopton, A., Federation, A., Marineau, J.J., Qi, J., Barsyte-Lovejoy, D., Yi, J., Marcellus, R., Iacob, R.E., Engen, J.R., Griffin, C., Aman, A., Wienholds, E., Li, F., Pineda, J., Estiu, G., Shatseva, T., Hajian, T., Al-Awar, R., Dick, J.E., Vedadi, M., Brown, P.J., Arrowsmith, C.H., Bradner, J.E., Schapira, M.

(2012) Nat Commun 3: 1288-1288

PubMed: 23250418 Search on PubMed
Primary Citation of Related Structures:
4ER7, 4ER6, 4ER5, 4ER3, 4ER0, 3UWP

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone-lysine N-methyltransferase, H3 lysine-79 specific	A	421	Homo sapiens	Mutation(s): 0 Gene Names: DOT1L (KIAA1814, KMT4) EC: 2.1.1.43
Find proteins for Q8TEK3 (Homo sapiens) Go to Gene View: DOT1L Go to UniProtKB: Q8TEK3
Protein Feature View Full Protein Feature View for Q8TEK3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
AW0 Query on AW0 Download SDF File Download CCD File	A	5'-deoxy-5'-[(3-{[(4-methylphenyl)carbamoyl]amino}propyl)(propan-2-yl)amino]adenosine C₂₄ H₃₄ N₈ O₄ KQTSVJQPAVOUSL-ZDXOVATRSA-N		Ligand Interaction
UNX Query on UNX Download SDF File Download CCD File	A	UNKNOWN ATOM OR ION X *		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.221
R-Value Work: 0.199
Space Group: P 6₅

Unit Cell:

Length (Å)	Angle (°)
a = 150.009	α = 90.00
b = 150.009	β = 90.00
c = 53.244	γ = 120.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
XSCALE	data scaling
SCALA	data scaling
REFMAC	refinement
Blu-Ice	data collection

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

Deposited Date: 2012-04-19
Released Date: 2012-05-02
Deposition Author(s): Wernimont, A.K., Tempel, W., Yu, W., Li, Y., Nguyen, K.T., Federation, A., Marineau, J., Qi, J., Vedadi, M., Bradner, J.E., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Brown, P.J., Structural Genomics Consortium (SGC)

Revision History

Version 1.0: 2012-05-02
Type: Initial release
Version 1.1: 2017-11-15
Type: Refinement description
Version 1.2: 2018-05-16
Type: Data collection, Database references

The RCSB PDB is funded by a grant (DBI-1338415) from the National Science Foundation, the National Institutes of Health, and the US Department of Energy.