11HQ | pdb_000011hq

Type-III c-MET Inhibitor Enabled by Free-Energy Perturbation Calculations

PDB DOI: https://doi.org/10.2210/pdb11HQ/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2026-02-25 Released: 2026-05-27
Deposition Author(s): Eiler, D.R., Abraham, N., Kutter, S., Kroeck, K.G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.287 (Depositor), 0.286 (DCC)
R-Value Work:
0.223 (Depositor), 0.224 (DCC)

Starting Model: experimental
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Literature

Discovery of 2H-Pyrrolo[3,4-c]pyridin-3-one Derivatives as Type-III c-MET Inhibitors Enabled by Free-Energy Perturbation Calculations

Therrien, E., Feng, S., Amberg-Johnson, K., Shaikh, N., Patil, P., Majumdar, S., Abraham, N., Eiler, D., Kutter, S., Albanese, S.K., Haldar, S., Kroeck, K.G., Atsriku, C., Gerasyuto, A.I., Levinson, A.M.

(2026) ACS Med Chem Lett

DOI: https://doi.org/10.1021/acsmedchemlett.6c00158

Macromolecule Content

Total Structure Weight: 105.98 kDa
Atom Count: 6,492
Modeled Residue Count: 802
Deposited Residue Count: 930
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A, B, C	310	Homo sapiens	Mutation(s): 1 Gene Names: MET EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P08581 (Homo sapiens) Explore P08581 Go to UniProtKB: P08581
PHAROS: P08581 GTEx: ENSG00000105976
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08581
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1C9B (Subject of Investigation/LOI) Query on A1C9B Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	(1R,6M)-1-benzyl-6-[(3P)-3-(1-ethyl-1H-pyrazol-4-yl)-5-fluorophenyl]-1,2-dihydro-3H-pyrrolo[3,4-c]pyridin-3-one C₂₅ H₂₁ F N₄ O CUVJLVPIGUUZFL-XMMPIXPASA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.287 (Depositor), 0.286 (DCC)
R-Value Work: 0.223 (Depositor), 0.224 (DCC)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.329	α = 90
b = 81.357	β = 90
c = 254.314	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-05-27
Type: Initial release

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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.