Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 34.68 kDa 
• Atom Count: 2331 
• Modelled Residue Count: 267 
• Deposited Residue Count: 299 
• Unique protein chains: 1

3VBT

Exploitation of hydrogen bonding constraints and flat hydrophobic energy landscapes in Pim-1 kinase needle screening and inhibitor design

• DOI: 10.2210/pdb3VBT/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-02 Released: 2012-03-21 
• Deposition Author(s): Liu, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.273 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 

Literature

Implications of promiscuous Pim-1 kinase fragment inhibitor hydrophobic interactions for fragment-based drug design.

Good, A.C., Liu, J., Hirth, B., Asmussen, G., Xiang, Y., Biemann, H.P., Bishop, K.A., Fremgen, T., Fitzgerald, M., Gladysheva, T., Jain, A., Jancsics, K., Metz, M., Papoulis, A., Skerlj, R., Stepp, J.D., Wei, R.R.

(2012) J Med Chem 55: 2641-2648

• PubMed: 22339127 
• DOI: 10.1021/jm2014698
• Primary Citation of Related Structures:  
  3VBQ, 3VBT, 3VBV, 3VBW, 3VBX, 3VBY, 3VC4


• PubMed Abstract: 
  

We have studied the subtleties of fragment docking and binding using data generated in a Pim-1 kinase inhibitor program. Crystallographic and docking data analyses have been undertaken using inhibitor complexes derived from an in-house surface plasmon resonance (SPR) fragment screen, a virtual needle screen, and a de novo designed fragment inhibitor hybrid. These investigations highlight that fragments that do not fill their binding pocket can exhibit promiscuous hydrophobic interactions due to the lack of steric constraints imposed on them by the boundaries of said pocket. As a result, docking modes that disagree with an observed crystal structure but maintain key crystallographically observed hydrogen bonds still have potential value in ligand design and optimization. This observation runs counter to the lore in fragment-based drug design that all fragment elaboration must be based on the parent crystal structure alone.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Genzyme Corp., 153 Second Avenue, Waltham, Massachusetts 02451, United States. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase pim-1	A	299	Homo sapiens	Mutation(s): 0  Gene Names: PIM1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens) Explore P11309  Go to UniProtKB:  P11309
PHAROS:  P11309 GTEx:  ENSG00000137193

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0F9 (Subject of Investigation/LOI)	B [auth A]	4-chloro-2-(1H-pyrazol-3-yl)phenol C9 H7 Cl N2 O DMGLUMYOLOAXJY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0F9	Binding MOAD:  3VBT	IC50: 3.70e+4 (nM) from 1 assay(s)
	PDBBind:  3VBT	IC50: 3.70e+4 (nM) from 1 assay(s)
	BindingDB:  3VBT	IC50: 3.70e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.273 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97	α = 90
b = 97	β = 90
c = 81	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2012-01-02 
• Released Date: 2012-03-21 
Deposition Author(s): Liu, J.

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2012-05-16
  Changes: Database references