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6xvb

Crystal structure of the kinase domain of human c-KIT with a cyclic imidate inhibitor covalently bound to Cys788

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Mast/stem cell growth factor receptor Kit,Mast/stem cell growth factor receptor Kit

Homo sapiens

UniProt P10721

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 ~{N}-(4,4-dimethyl-2-propyl-3,1-benzoxazin-6-yl)-2-[3-methoxy-5-(7-methoxyquinolin-4-yl)oxy-pyridin-2-yl]ethanamide × 1 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 ~{N}-(4,4-dimethyl-2-propyl-3,1-benzoxazin-6-yl)-2-[3-methoxy-5-(7-methoxyquinolin-4-yl)oxy-pyridin-2-yl]ethanamide × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1pkg 1pkg 1t45 1t46 2ec8 3g0e 4hvs 4u0i 6gqj 6gqj 6gqk 6gqk

55 assemblies; showing the first 12

Homodimer
3g0f 4hvs 4pgz 4pgz 6itt 6itv 6kla

7 assemblies

Homotetramer
1pkg 3g0f

2 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
2e9w 2vif 4k94 4k9e 8dfm 8dfp 8dfq 9h71 9h71

9 assemblies

View Construct and Data Evidence
UniProt name KIT_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–141； UniProt 551–687 Author chain A； PDBConstruct 160–328； UniProt 766–934 Author chain B； PDBConstruct 5–141； UniProt 551–687 Author chain B； PDBConstruct 160–328； UniProt 766–934

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id6xvb
Deposition date deposition_date2020-01-21
Structure title titleCrystal structure of the kinase domain of human c-KIT with a cyclic imidate inhibitor covalently bound to Cys788
Keywords keywordstype II kinase inhibitor, structure-based drug design, covalent inhibitor, cysteine reactive warhead, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6xvb__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6xvb__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6xvb__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）20.53 Å
Rg (electron density)19.40 Å
Total Rg20.39 Å
Atom count2401
Residues297
Excluded volume42978 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6xvb__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6xvb__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

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6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6xvba_
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
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7. Citations (1)