Macromolecule Content

Total Structure Weight: 64.73 kDa
Atom Count: 4,238
Modelled Residue Count: 518
Deposited Residue Count: 562
Unique protein chains: 1

2FB8

Structure of the B-Raf kinase domain bound to SB-590885

PDB DOI: https://doi.org/10.2210/pdb2FB8/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2005-12-08 Released: 2006-12-12
Deposition Author(s): Lougheed, J.C., Lee, J., Chau, D.C., Stout, T.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.291
R-Value Work: 0.199
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Demonstration of a genetic therapeutic index for tumors expressing oncogenic BRAF by the kinase inhibitor SB-590885.

King, A.J., Patrick, D.R., Batorsky, R.S., Ho, M.L., Do, H.T., Zhang, S.Y., Kumar, R., Rusnak, D.W., Takle, A.K., Wilson, D.M., Hugger, E., Wang, L., Karreth, F., Lougheed, J.C., Lee, J., Chau, D., Stout, T.J., May, E.W., Rominger, C.M., Schaber, M.D., Luo, L., Lakdawala, A.S., Adams, J.L., Contractor, R.G., Smalley, K.S., Herlyn, M., Morrissey, M.M., Tuveson, D.A., Huang, P.S.

(2006) Cancer Res 66: 11100-11105

PubMed: 17145850 Search on PubMed
DOI: https://doi.org/10.1158/0008-5472.CAN-06-2554
Primary Citation of Related Structures:
2FB8

PubMed Abstract:

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-Raf proto-oncogene serine/threonine-protein kinase	A, B	281	Homo sapiens	Mutation(s): 0 Gene Names: BRAF, BRAF1, RAFB1 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens) Explore P15056 Go to UniProtKB: P15056
PHAROS: P15056
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15056
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
215 Query on 215 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	(1Z)-5-(2-{4-[2-(DIMETHYLAMINO)ETHOXY]PHENYL}-5-PYRIDIN-4-YL-1H-IMIDAZOL-4-YL)INDAN-1-ONE OXIME C₂₇ H₂₇ N₅ O₂ MLSAQOINCGAULQ-QLTSDVKISA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
215	PDBBind: 2FB8	Kd: 0.16 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.291
R-Value Work: 0.199
R-Value Observed: 0.203
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.638	α = 90
b = 95.638	β = 90
c = 159.222	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-12-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-12-12
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance

RCSB PDB Core Operations are 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.