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 12FF | pdb_000012ff

KRAS G12V in complex with GDP and a macrocyclic inhibitor (Compound 20).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.274 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 12FF

Ligand Structure Quality Assessment 


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

Literature

Lead Optimization of Multimutant KRAS Switch-II Pocket Macrocyclic Inhibitors via Isosteric Replacement to Improve ADME and Oral Exposure.

Phillips, D.P., Alper, P.B., Borkin, D., Han, D., Kochanek, S.E., Gurjar, J., Mathison, C.J.N., Nelson, J.M., Pei, W., Nguyen, B.N., Hoffman, T., Okram, B., Nguyen, T.N., Jiang, S., Masick, B.T., Wang, Z., Cho, C.Y., Yin, H., Chen, Y., Juarez, J., Jia, Y., Zhou, V., Liu, G., Wright, C., Nguyen, T., Knee, D.A., Liu, Q., Liu, J., Li, J., Virata, C., de Oliveira, C., DiDonato, M., Bursulaya, B., Vidal-Biggart, A., Jones, D.H., Witmer, D., Chu, C., Jin, H., Herath, A., Richmond, W., Groessl, T., Shapiro, M., Effenberger, K., Arroyo, K., Bretz, A., Honda, A., Gordon, W.P., Molteni, V., Haling, J.R.

(2026) J Med Chem 69: 20698-20718

  • DOI: https://doi.org/10.1021/acs.jmedchem.6c01454
  • Primary Citation Related Structures: 
    12FF, 12FG

  • PubMed Abstract: 

    Starting from our internally discovered, potent panKRAS inhibitor BRSD-143 (1), we executed a targeted bioisosteric optimization of the naphthol and fluoropyrrolizidine motifs to preserve (or increase) KRAS pan-inhibitory potency while improving DMPK/ADME liabilities. These studies delivered 12 (BRSD-212), a highly potent and efficacious lead in which (2-azabicyclo[4.2.0]octan-6-yl)methanol (ABO) serves as a bioisostere for the widely deployed 2-fluoropyrrolizidine substituent. In parallel, replacement of the naphthol moiety with an indazole afforded 21, which demonstrated improved pharmacokinetic performance and ADME characteristics by mitigating glucuronidation-mediated clearance as the dominant metabolic pathway.


  • Organizational Affiliation: 
    • Novartis Biomedical Research , 10675 John Jay Hopkins Drive, San Diego, California92121, United States.

Macromolecule Content 

  • Total Structure Weight: 82.42 kDa 
  • Atom Count: 6,091 
  • Modeled Residue Count: 672 
  • Deposited Residue Count: 684 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2B of GTPase KRas
A, B, C, D
171Homo sapiensMutation(s): 4 
Gene Names: KRAS, KRAS2, RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1DB0
(Subject of Investigation/LOI)

Query on A1DB0



Download:Ideal Coordinates CCD File
F [auth A],
K [auth B],
P [auth C],
T [auth D]
(5S,9R,21bP)-25-fluoro-3-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}-9-methyl-7,8,9,10,14,15,16,19-octahydro-13H-5,9-methano-22,1-(metheno)pyrimido[4',5':9,10][1,3,8]oxadiazacyclononadecino[14,15-e]indazol-11(6H)-one
C34 H39 F2 N7 O3
UGFJXOPXCUKURZ-NMUJKEQYSA-N
GDP

Query on GDP



Download:Ideal Coordinates CCD File
G [auth A],
L [auth B],
Q [auth C],
U [auth D]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
M [auth B]
N [auth B]
R [auth C]
H [auth A],
I [auth A],
M [auth B],
N [auth B],
R [auth C],
V [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B],
O [auth C],
S [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.274 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.418α = 95.725
b = 40.037β = 94.661
c = 122.427γ = 102.434
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-09
    Type: Initial release
  • Version 1.1: 2026-09-23
    Changes: Database references