3IPY | pdb_00003ipy

X-Ray structure of Human Deoxycytidine Kinase in complex with an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3IPY/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2009-08-18 Released: 2010-08-18 
• Deposition Author(s): Tari, L.W., Swanson, R.V., Hunter, M., Hoffman, I., Stouch, T.R., Carson, K.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 
  0.273 (Depositor) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Lead optimization and structure-based design of potent and bioavailable deoxycytidine kinase inhibitors.

Jessop, T.C., Tarver, J.E., Carlsen, M., Xu, A., Healy, J.P., Heim-Riether, A., Fu, Q., Taylor, J.A., Augeri, D.J., Shen, M., Stouch, T.R., Swanson, R.V., Tari, L.W., Hunter, M., Hoffman, I., Keyes, P.E., Yu, X.C., Miranda, M., Liu, Q., Swaffield, J.C., David Kimball, S., Nouraldeen, A., Wilson, A.G., Foushee, A.M., Jhaver, K., Finch, R., Anderson, S., Oravecz, T., Carson, K.G.

(2009) Bioorg Med Chem Lett 19: 6784-6787

• PubMed: 19836232 
• DOI: https://doi.org/10.1016/j.bmcl.2009.09.081
• Primary Citation of Related Structures:  
  3IPX, 3IPY


• PubMed Abstract: 
  

  A series of deoxycytidine kinase inhibitors was simultaneously optimized for potency and PK properties. A co-crystal structure then allowed merging this series with a high throughput screening hit to afford a highly potent, selective and orally bioavailable inhibitor, compound 10. This compound showed dose dependent inhibition of deoxycytidine kinase in vivo.

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Organizational Affiliation: 

Lexicon Pharmaceuticals, Princeton, NJ 08540, United States. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.15 kDa 
• Atom Count: 3,987 
• Modelled Residue Count: 450 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxycytidine kinase	A, B	241	Homo sapiens	Mutation(s): 0  EC: 2.7.1.74 (PDB Primary Data), 2.7.1.113 (UniProt), 2.7.1.76 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P27707 (Homo sapiens) Explore P27707  Go to UniProtKB:  P27707
PHAROS:  P27707 GTEx:  ENSG00000156136

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B87	D [auth A], E [auth A], G [auth B], H [auth B]	4-(1-benzothiophen-2-yl)-6-[4-(2-oxo-2-pyrrolidin-1-ylethyl)piperazin-1-yl]pyrimidine C22 H25 N5 O S NDLZMZLRTHDNSQ-UHFFFAOYSA-N
MLT	C [auth A], F [auth B]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
B87	BindingDB:  3IPY	IC50: min: 510, max: 5.10e+5 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free:  0.273 (Depositor) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.556	α = 90
b = 74.428	β = 90
c = 239.097	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Tari, L.W., Swanson, R.V., Hunter, M., Hoffman, I., Stouch, T.R., Carson, K.G.

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description