2c3j

Identification of a buried pocket for potent and selective inhibition of Chk1: prediction and verification

Method: X-RAY DIFFRACTION Dmax: 65.5 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

SERINE/THREONINE-PROTEIN KINASE CHK1

HOMO SAPIENS

UniProt O14757

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–289 Fragment:N-TERMINAL KINASE DOMAIN, RESIDUES 1-289 DBQ DEBROMOHYMENIALDISINE × 1 SO3 SULFITE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;pH 7.50 Resolution 2.10 Å R-free 0.262

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

162 other PDB entries and 172 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CHK1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–289; UniProt 1–289

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2c3j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2c3j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2c3j
Deposition date deposition_date2005-10-10
Structure title titleIdentification of a buried pocket for potent and selective inhibition of Chk1: prediction and verification
Keywords keywords;DRUG DESIGN, MOLECULAR MODELING, MOLECULAR RECOGNITION, ONCOLOGY, TRANSFERASE, CELL CYCLE, DNA DAMAGE, DNA REPAIR, ATP-BINDING, KINASE, NUCLEAR PROTEIN, NUCLEOTIDE-BINDING, PHOSPHORYLATION, POLYMORPHISM, SERINE/THREONINE-PROTEIN KINASE, UBL CONJUGATION ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.29
Radius of gyration Rg (electron density) rg_electron19.21
Forward intensity I(0) i015434700.00
Molecular weight molecular_weight29948.0 kDa
Excluded volume excluded_volume37618 ų
Envelope volume envelope_volume43830 ų
Hydration-shell volume shell_volume19289 ų
Envelope diameter envelope_diameter67.6
Shell Rg shell_rg25.26
Envelope Rg envelope_rg19.53
Shape Rg shape_rg19.21
Total Rg total_rg20.09
Total atoms total_atoms2109
Residues n_residues257
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax65.5
Rg (real space) rg_real20.24
Rg uncertainty (real space) rg_real_error0.46
I(0) (real space) i0_real1.5430e+07
I(0) uncertainty (real space) i0_real_error1.8540e+05
Rg (reciprocal space) rg_reciprocal20.25
I(0) (reciprocal space) i0_reciprocal15430000.0000
Solution quality estimate total_estimate0.8165
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.3
Skewness Skewness skewness0.287
Kurtosis Kurtosis kurtosis-0.345
Angular range angular_range— – 0.3900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3775000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.870; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2c3ja_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (2 domains)

Domain ID domain_id2c3jA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id2c3jA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1

8. Citations (1)

9. Files and Curves (10)