Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.95 kDa 
• Atom Count: 2,739 
• Modelled Residue Count: 332 
• Deposited Residue Count: 366 
• Unique protein chains: 1

 3P7C

p38 inhibitor-bound

• PDB DOI: 10.2210/pdb3P7C/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-10-12 Released: 2011-10-12 
• Deposition Author(s): Moffett, K.K., Namboodiri, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.292 
• R-Value Work: 0.234 
• R-Value Observed: 0.239 

Literature

Discovery of a novel class of non-ATP site DFG-out state p38 inhibitors utilizing computationally assisted virtual fragment-based drug design (vFBDD).

Moffett, K., Konteatis, Z., Nguyen, D., Shetty, R., Ludington, J., Fujimoto, T., Lee, K.J., Chai, X., Namboodiri, H., Karpusas, M., Dorsey, B., Guarnieri, F., Bukhtiyarova, M., Springman, E., Michelotti, E.

(2011) Bioorg Med Chem Lett 21: 7155-7165

• PubMed: 22014550 
• DOI: 10.1016/j.bmcl.2011.09.078
• Primary Citation of Related Structures:  
  3P5K, 3P78, 3P79, 3P7A, 3P7B, 3P7C


• PubMed Abstract: 
  

Discovery of a new class of DFG-out p38α kinase inhibitors with no hinge interaction is described. A computationally assisted, virtual fragment-based drug design (vFBDD) platform was utilized to identify novel non-aromatic fragments which make productive hydrogen bond interactions with Arg 70 on the αC-helix. Molecules incorporating these fragments were found to be potent inhibitors of p38 kinase. X-ray co-crystal structures confirmed the predicted binding modes. A lead compound was identified as a potent (p38α IC(50)=22 nM) and highly selective (≥ 150-fold against 150 kinase panel) DFG-out p38 kinase inhibitor.

---

Organizational Affiliation: 

Ansaris, Four Valley Square, 512 East Township Line Road, Blue Bell, PA 19422, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	366	Mus musculus	Mutation(s): 0  Gene Names: Mapk14, Crk1, Csbp1, Csbp2 EC: 2.7.11.24
UniProt
Find proteins for P47811 (Mus musculus) Explore P47811  Go to UniProtKB:  P47811

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P7C	C [auth A]	1-[5-tert-butyl-3-({4-[2-(dimethylamino)ethyl]-5-oxo-1,4-diazepan-1-yl}carbonyl)thiophen-2-yl]-3-(2,3-dichlorophenyl)urea C25 H33 Cl2 N5 O3 S SIUIQMQVKUUQQF-UHFFFAOYSA-N
BOG	B [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
P7C	Binding MOAD:  3P7C	IC50: 22 (nM) from 1 assay(s)
	PDBBind:  3P7C	IC50: 22 (nM) from 1 assay(s)
	BindingDB:  3P7C	IC50: 22 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.292 
• R-Value Work: 0.234 
• R-Value Observed: 0.239 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.86	α = 90
b = 70.77	β = 90
c = 76.13	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Moffett, K.K., Namboodiri, H.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2011-11-09
  Changes: Database references
• Version 1.2: 2012-01-25
  Changes: Database references
• Version 1.3: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary