10MV | pdb_000010mv

N-Alkyl & N-Aryl Aminopyrazole Spirocarbamates: A Two-Pronged Lead Optimization Strategy to Identify Orally Bioavailable Plasma Kallikrein Inhibitors complex with Compound 15 ((3'R)-1'-(5-amino-1-phenyl-1H-pyrazole-4-carbonyl)-6-chloro-5-fluorospiro[[3,1]benzoxazine-4,3'-piperidin]-2(1H)-one)

• PDB DOI: https://doi.org/10.2210/pdb10MV/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2026-01-28 Released: 2026-04-01 
• Deposition Author(s): Merchant, R.R., Chernyak, N., Lopez, J.A., Sharp, P.P., Mandal, M., He, J., Hruza, A., Rearden, P., Tatosian, D.A., Lin, K., Esmay, J., Yang, S., Cheng, A., Ellsworth, K., Ogawa, A., Piou, T., Fier, P., Hicks, J., Sinz, C., Ogawa, A.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.226 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.204 (DCC) 

Starting Model: experimental

Literature

N ‐Alkyl and N ‐Aryl Aminopyrazole Spirocarbamates: A Two-Pronged Lead Optimization Strategy to Identify Orally Bioavailable Plasma Kallikrein Inhibitors.

Merchant, R.R., Chernyak, N., Lopez, J.A., Sharp, P.P., Mandal, M., He, J., Hruza, A., Rearden, P., Tatosian, D.A., Esmay, J., Yang, S., Cheng, A.C., Ellsworth, K., Ogawa, A., Piou, T., Fier, P., Hicks, J., Sinz, C., Ogawa, A.K.

(2026) ACS Med Chem Lett 17: 744-749

• PubMed: 41847638 
• DOI: https://doi.org/10.1021/acsmedchemlett.6c00066
• Primary Citation Related Structures: 
  10KZ, 10LR, 10MV, 10MW, 10QS


• PubMed Abstract: 
  

  Plasma kallikrein (pKal) is a trypsin-like serine protease involved in the kallikrein-kinin, renin-angiotensin, and complement pathways, making it an attractive target for diseases, such as hereditary angioedema, diabetic mellitus complications, and cerebrovascular disorders. As part of an internal program to develop orally bioavailable small-molecule pKal inhibitors, we report lead optimization efforts within the spirocarbamate scaffold, highlighting a structure-based drug design strategy to engineer hydrogen bond interactions with N -benzyl aminopyrazoles. Additionally, mitigation of time-dependent inhibition (TDI) liability and optimization of the overall profile were achieved through a two-pronged strategy: (1) incorporating increased Fsp ³ modifications via N -alkylation and (2) leveraging torsional strain in N -aryl analogs.

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Organizational Affiliation: 
• Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States.
Department of Discovery Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States.
Pharmacokinetics, Dynamics, Metabolism and Bioanalytics, Merck & Co., Inc., South San Francisco, California 94080, United States.
Pharmacokinetics, Dynamics, Metabolism and Bioanalytics, Merck & Co., Inc., Rahway, New Jersey 07065, United States.
Computational and Structural Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States.
Quantitative Biosciences, Merck & Co., Inc., Rahway, New Jersey 07065, United States.
Quantitative Biosciences, Merck & Co., Inc., South San Francisco, California 94080, United States.
Department of Process Research and Development, 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.75 kDa 
• Atom Count: 2,032 
• Modeled Residue Count: 231 
• Deposited Residue Count: 275 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasma kallikrein	A	275	Homo sapiens	Mutation(s): 2  Gene Names: KLKB1, KLK3 EC: 3.4.21.34
UniProt & NIH Common Fund Data Resources
Find proteins for P03952 (Homo sapiens) Explore P03952  Go to UniProtKB:  P03952
PHAROS:  P03952 GTEx:  ENSG00000164344
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P03952-1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1C6X (Subject of Investigation/LOI)	C [auth A]	(3'R)-1'-(5-amino-1-phenyl-1H-pyrazole-4-carbonyl)-6-chloro-5-fluorospiro[[3,1]benzoxazine-4,3'-piperidin]-2(1H)-one C22 H19 Cl F N5 O3 UIAVIEYDGWFKJG-QFIPXVFZSA-N
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MES	B [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.226 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.204 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.474	α = 90
b = 77.959	β = 90
c = 47.465	γ = 90

Software Package:

Software Name	Purpose
autoBUSTER	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-01 
Deposition Author(s): Merchant, R.R., Chernyak, N., Lopez, J.A., Sharp, P.P., Mandal, M., He, J., Hruza, A., Rearden, P., Tatosian, D.A., Lin, K., Esmay, J., Yang, S., Cheng, A., Ellsworth, K., Ogawa, A., Piou, T., Fier, P., Hicks, J., Sinz, C., Ogawa, A.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2026-04-01
  Type: Initial release