11IH | pdb_000011ih

CYP8B1 inhibitor compound 1

• PDB DOI: https://doi.org/10.2210/pdb11IH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2026-02-25 Released: 2026-10-28 
• Deposition Author(s): Hruza, A., Orth, P.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.225 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Structure-Based Drug Design of Quinoline CYP8B1 Inhibitors for the Potential Treatment of Metabolic Disease.

McCracken, A.B., Li, D., Caldwell, J.P., Lankin, C., Tagat, J., Khan, T., Rao, A., Zhang, T., Caplen, M.A., Verras, A., Orth, P., Hruza, A., Ho, T., Allen, S., Elsen, N.L., Dingley, K., Duffy, R., Wisniewski, T., Murphy, B., Castro-Perez, J., Wong, K., Streckfuss, E., Liu, J., Tong, W., McKittrick, B.

(2026) ACS Med Chem Lett 17: 2245-2250

• PubMed: 42866422 
• DOI: https://doi.org/10.1021/acsmedchemlett.6c00387
• Primary Citation Related Structures: 
  11IH, 11IR


• PubMed Abstract: 
  

  CYP8B1 has been identified as a potential target for the treatment of metabolic diseases, such as nonalcoholic fatty liver disease (NAFLD) and type 2 diabetes (T2D). CYP8B1 enzyme inhibitor 1 was discovered from a high-throughput screen of our compound collection; however, its poor metabolic stability prevented further in vivo evaluation. Leveraging structure-based drug design, metabolite identification and metabolic stability-guided DMPK optimization, and library synthesis to rapidly expand SAR, we identified compound 9 with substantially improved DMPK properties. Compound 9 showed robust in vivo CYP8B1 inhibition in mice and provided the foundation for further optimization of this class of CYP8B1 inhibitors.

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Organizational Affiliation: 
• Merck & Co., Inc., Rahway, New Jersey 07065, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 57.98 kDa 
• Atom Count: 4,091 
• Modeled Residue Count: 461 
• Deposited Residue Count: 488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7-alpha-hydroxycholest-4-en-3-one 12-alpha-hydroxylase	A	488	Homo sapiens	Mutation(s): 0  Gene Names: CYP8B1, CYP12 EC: 1.14.14.139
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNU6 (Homo sapiens) Explore Q9UNU6  Go to UniProtKB:  Q9UNU6
PHAROS:  Q9UNU6 GTEx:  ENSG00000180432

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
A1C9D( Subject of Investigation/LOI)	C [auth A]	6-methyl-4-[4-(4-methylpiperidine-1-carbonyl)piperidin-1-yl]quinoline-3-carbonitrile C23 H28 N4 O BJGUYZVGGPNEGT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.225 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.844	α = 90
b = 89.708	β = 90
c = 106.436	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Hruza, A., Orth, P.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release