3GCS
Human P38 MAP kinase in complex with Sorafenib
- PDB DOI: https://doi.org/10.2210/pdb3GCS/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): Yes 
- Deposited: 2009-02-22 Released: 2009-06-09 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.262 
- R-Value Work: 0.202 
- R-Value Observed: 0.204 
This is version 1.5 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Mitogen-activated protein kinase 14 | 360 | Homo sapiens | Mutation(s): 4  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2 EC: 2.7.11.24 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539 | |||||
PHAROS:  Q16539 GTEx:  ENSG00000112062  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q16539 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
BAX Query on BAX | B [auth A] | 4-{4-[({[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}-N-METHYLPYRIDINE-2-CARBOXAMIDE C21 H16 Cl F3 N4 O3 MLDQJTXFUGDVEO-UHFFFAOYSA-N | |||
BOG Query on BOG | C [auth A] | octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N |
Binding Affinity Annotations  | |||
---|---|---|---|
ID | Source | Binding Affinity | |
BAX | PDBBind:  3GCS | Kd: 56 (nM) from 1 assay(s) | |
BindingDB:  3GCS | Kd: min: 260, max: 1.00e+4 (nM) from 3 assay(s) | ||
IC50: min: 37, max: 3200 (nM) from 7 assay(s) | |||
Binding MOAD:  3GCS | Kd: 56 (nM) from 1 assay(s) |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.262 
- R-Value Work: 0.202 
- R-Value Observed: 0.204 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 67.48 | α = 90 |
b = 69.85 | β = 90 |
c = 74.8 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data scaling |
XSCALE | data scaling |
Entry History 
Deposition Data
- Released Date: 2009-06-09  Deposition Author(s): Gruetter, C., Simard, J.R., Rauh, D.
Revision History (Full details and data files)
- Version 1.0: 2009-06-09
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 1.4: 2021-10-20
Changes: Database references, Structure summary - Version 1.5: 2023-09-06
Changes: Data collection, Refinement description