31ZN | pdb_000031zn

Structure of CDK11-cyclin L-SAP30BP in complex with IACS-054647

• PDB DOI: https://doi.org/10.2210/pdb31ZN/pdb
• EM Map EMD-58734: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2026-06-30 Released: 2026-08-19 
• Deposition Author(s): McGeoch, A.J.S., Greber, B.J., Sheltzer, J.M.
• Funding Organization(s): The Institute of Cancer Research (ICR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

A genetic platform to deconvolve efficacy and toxicity reveals the on-target effects of CDK11 inhibition in vivo

Julian, L., Crozier, L., Lukow, D., Swamy, A., Mishra, S., Hagenson, R.A., Sennhenn, P., Sausville, E.L., McGeoch, A.J.S., Thompson, S.L., Mendelson, B., Chuaqui, C., Qiao, L., Vasudevan, A., Lin, K.T., Bhatia, S., Bertomeu, T., Chatr-aryamontri, A., Zhang, L., Rees, M.G., Ronan, M.M., Roth, J.A., Nottoli, T., Bai, S., Lakshmipathi, J., Muthusamy, V., Van Vranken, J.G., Gauthier-Coles, G., Gygi, S.P., Smith, J.C., Anderson, K., Shah, S., Bindra, R.S., Akerman, M., Spector, D.L., Greber, B.J., Krainer, A.R., Sheltzer, J.M.

(2026) Nat Commun 

• DOI: https://doi.org/10.1038/s41467-026-78814-0

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 120.17 kDa 
• Atom Count: 5,326 
• Modeled Residue Count: 649 
• Deposited Residue Count: 1,075 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAP30-binding protein	A	311	Homo sapiens	Mutation(s): 0  Gene Names: SAP30BP, HCNGP, HTRG, HTRP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHR5 (Homo sapiens) Explore Q9UHR5  Go to UniProtKB:  Q9UHR5
PHAROS:  Q9UHR5 GTEx:  ENSG00000161526

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 7 of Cyclin-dependent kinase 11B	B	442	Homo sapiens	Mutation(s): 0  Gene Names: CDK11B, CDC2L1, CDK11, PITSLREA, PK58 EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P21127 (Homo sapiens) Explore P21127  Go to UniProtKB:  P21127
GTEx:  ENSG00000248333

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-L2	C	322	Homo sapiens	Mutation(s): 0  Gene Names: CCNL2, SB138
UniProt & NIH Common Fund Data Resources
Find proteins for Q96S94 (Homo sapiens) Explore Q96S94  Go to UniProtKB:  Q96S94
PHAROS:  Q96S94 GTEx:  ENSG00000221978

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1KC9 (Subject of Investigation/LOI)	D [auth B]	4-[8-[[(3~{S})-piperidin-3-yl]amino]imidazo[1,2-a]pyridin-6-yl]benzenecarbonitrile C19 H19 N5 UOXKWAOIRXHSBN-KRWDZBQOSA-N

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
TPO	B	THR	Phosphorylation	C4 H10 N O6 P

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	RELION	5.0.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-19 
Deposition Author(s): McGeoch, A.J.S., Greber, B.J., Sheltzer, J.M.

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Funding Organization	Location	Grant Number
The Institute of Cancer Research (ICR)	United Kingdom	--

Revision History  

• Version 1.0: 2026-08-19
  Type: Initial release
  
• Version 1.1: 2026-11-04
  Changes: Data collection, Database references