Macromolecule Content

Total Structure Weight: 44.74 kDa
Atom Count: 3711
Modelled Residue Count: 366
Deposited Residue Count: 384
Unique protein chains: 1

6BG3

Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl acetate bound to DCN1

PDB DOI: 10.2210/pdb6BG3/pdb

Classification: HYDROLASE, LIGASE/INHIBITOR
Organism(s): Escherichia virus T4, Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-10-27 Released: 2018-09-26
Deposition Author(s): Guy, R.K., Schulman, B.A., Scott, D.C., Hammill, J.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.173
R-Value Work: 0.155
R-Value Observed: 0.157

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Piperidinyl Ureas Chemically Control Defective in Cullin Neddylation 1 (DCN1)-Mediated Cullin Neddylation.

Hammill, J.T., Scott, D.C., Min, J., Connelly, M.C., Holbrook, G., Zhu, F., Matheny, A., Yang, L., Singh, B., Schulman, B.A., Guy, R.K.

(2018) J Med Chem 61: 2680-2693

PubMed: 29547696 Search on PubMedSearch on PubMed Central
DOI: 10.1021/acs.jmedchem.7b01277
Primary Citation of Related Structures:
6BG3, 6BG5

PubMed Abstract:

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endolysin, DCN1-like protein 1 chimera	A	384	Escherichia virus T4, Homo sapiens This entity is chimeric	Mutation(s): 0 Gene Names: E, DCUN1D1, DCUN1L1, RP42, SCCRO EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720 Go to UniProtKB: P00720
Find proteins for Q96GG9 (Homo sapiens) Explore Q96GG9 Go to UniProtKB: Q96GG9
PHAROS: Q96GG9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q96GG9P00720
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DOJ Query on DOJ Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-{(3S,4S)-1-benzyl-3-[(1S)-1-hydroxyethoxy]piperidin-4-yl}-N'-[3-(trifluoromethyl)phenyl]urea C₂₂ H₂₆ F₃ N₃ O₃ KGJIMOVTOXSTNJ-YSSFQJQWSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
DOJ	Binding MOAD: 6BG3	IC50: 1.20e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.173
R-Value Work: 0.155
R-Value Observed: 0.157
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.169	α = 90
b = 96.915	β = 105.5
c = 59.388	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Deposited Date: 2017-10-27
Released Date: 2018-09-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-09-26
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.