7XBI | pdb_00007xbi

The crystal structure of human TrkA kinase bound to the inhibitor

PDB DOI: https://doi.org/10.2210/pdb7XBI/pdb

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

Deposited: 2022-03-21 Released: 2023-03-29
Deposition Author(s): Wu, C.Y., Wang, G., Ouyang, L.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.246 (Depositor), 0.246 (DCC)
R-Value Work:
0.188 (Depositor), 0.188 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of human TrkA kinase bound to the inhibitor

Wu, C.Y., Wang, G., Ouyang, L.

To be published.

Macromolecule Content

Total Structure Weight: 35.99 kDa
Atom Count: 2,527
Modeled Residue Count: 299
Deposited Residue Count: 311
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity nerve growth factor receptor	A	311	Homo sapiens	Mutation(s): 0 Gene Names: NTRK1, MTC, TRK, TRKA EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04629 (Homo sapiens) Explore P04629 Go to UniProtKB: P04629
PHAROS: P04629 GTEx: ENSG00000198400
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04629
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CVY (Subject of Investigation/LOI) Query on CVY Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-[[2-fluoranyl-5-(trifluoromethyl)phenyl]carbamoylamino]-~{N}-[3-(1-methylpyrazol-4-yl)-1~{H}-indazol-5-yl]-2-(trifluoromethyl)benzamide C₂₇ H₁₈ F₇ N₇ O₂ WTEUURGWUPJVOA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.246 (Depositor), 0.246 (DCC)
R-Value Work: 0.188 (Depositor), 0.188 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.01	α = 90
b = 52.01	β = 90
c = 229.51	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
autoXDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	81922064

Revision History (Full details and data files)

Version 1.0: 2023-03-29
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.