6PL4 | pdb_00006pl4

TRK-A IN COMPLEX WITH LIGAND 1

PDB DOI: https://doi.org/10.2210/pdb6PL4/pdb

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

Deposited: 2019-06-30 Released: 2020-07-01
Deposition Author(s): Subramanian, G., Brown, D.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.239 (Depositor), 0.237 (DCC)
R-Value Work:
0.199 (Depositor)
R-Value Observed:
0.202 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

In Pursuit of an Allosteric Human Tropomyosin Kinase A (hTrkA) Inhibitor for Chronic Pain

Subramanian, G., Duclos, B., Johnson, P.D., Williams, T., Ross, J.T., Bowen, S.J., Zhu, Y., White, J.A., Hedke, C., Huczek, D., Collard, W., Javens, C., Vairagoundar, R., Respondek, T., Zachary, T., Maddux, T., Cox, M.R., Kamerling, S., Gonzales, A.J.

(2021) ACS Med Chem Lett

DOI: https://doi.org/10.1021/acsmedchemlett.1c00483

Macromolecule Content

Total Structure Weight: 35.91 kDa
Atom Count: 2,570
Modeled Residue Count: 299
Deposited Residue Count: 311
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OO7 (Subject of Investigation/LOI) Query on OO7 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]	N-{[5-(methoxymethyl)-2-(trifluoromethoxy)phenyl]methyl}-N'-(8-methyl-2-phenylimidazo[1,2-a]pyrazin-3-yl)urea C₂₄ H₂₂ F₃ N₅ O₃ KNZNJSNITSGMNY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.239 (Depositor), 0.237 (DCC)
R-Value Work: 0.199 (Depositor)
R-Value Observed: 0.202 (Depositor)

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.052	α = 90
b = 52.052	β = 90
c = 227.917	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-07-01

Deposition Author(s):

Subramanian, G.

Revision History (Full details and data files)

Version 1.0: 2020-07-01
Type: Initial release
Version 1.1: 2021-11-03
Changes: Advisory, Database references, Refinement description
Version 1.2: 2024-10-30
Changes: Data collection, Structure summary

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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.