PDBsum entry 1h1p

Transferase

PDB id: 1h1p

Contents

Protein chains

297 a.a. *

258 a.a. *

Ligands

CMG ×2

Waters ×410

* Residue conservation analysis

PDB id:

1h1p

Name:

Transferase

Title:

Structure of human thr160-phospho cdk2/cyclin a complexed with the inhibitor nu2058

Structure:

Cell division protein kinase 2. Chain: a, c. Synonym: cyclin-dependent kinase 2, p33 protein kinase. Engineered: yes. Other_details: phosphorylated on thr160. Cyclin a2. Chain: b, d. Synonym: cyclin a, cyclin a3. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Dimer (from PDB file)

Resolution:

2.10Å R-factor: 0.222 R-free: 0.258

Authors:

T.G.Davies,M.E.M.Noble,J.A.Endicott,L.N.Johnson

Key ref:

T.G.Davies et al. (2002). Structure-based design of a potent purine-based cyclin-dependent kinase inhibitor. Nat Struct Biol, 9, 745-749. PubMed id: 12244298 DOI: 10.1038/nsb842

Date:

21-Jul-02 Release date: 19-Sep-02

Protein chains

P24941  (CDK2_HUMAN) -  Cyclin-dependent kinase 2 from Homo sapiens

Seq: 298 a.a.

Struc: 297 a.a.*

Protein chains

P20248  (CCNA2_HUMAN) -  Cyclin-A2 from Homo sapiens

Seq: 432 a.a.

Struc: 258 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, C: E.C.2.7.11.22 - cyclin-dependent kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] (Bound ligand (Het Group name = CMG) matches with 40.62% similarity) + ADP + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nsb842

Nat Struct Biol 9:745-749 (2002)

PubMed id: 12244298

Structure-based design of a potent purine-based cyclin-dependent kinase inhibitor.

T.G.Davies, J.Bentley, C.E.Arris, F.T.Boyle, N.J.Curtin, J.A.Endicott, A.E.Gibson, B.T.Golding, R.J.Griffin, I.R.Hardcastle, P.Jewsbury, L.N.Johnson, V.Mesguiche, D.R.Newell, M.E.Noble, J.A.Tucker, L.Wang, H.J.Whitfield.

ABSTRACT

Aberrant control of cyclin-dependent kinases (CDKs) is a central feature of the molecular pathology of cancer. Iterative structure-based design was used to optimize the ATP- competitive inhibition of CDK1 and CDK2 by O(6)-cyclohexylmethylguanines, resulting in O(6)-cyclohexylmethyl-2-(4'- sulfamoylanilino)purine. The new inhibitor is 1,000-fold more potent than the parent compound (K(i) values for CDK1 = 9 nM and CDK2 = 6 nM versus 5,000 nM and 12,000 nM, respectively, for O(6)-cyclohexylmethylguanine). The increased potency arises primarily from the formation of two additional hydrogen bonds between the inhibitor and Asp 86 of CDK2, which facilitate optimum hydrophobic packing of the anilino group with the specificity surface of CDK2. Cellular studies with O(6)-cyclohexylmethyl-2-(4'- sulfamoylanilino) purine demonstrated inhibition of MCF-7 cell growth and target protein phosphorylation, consistent with CDK1 and CDK2 inhibition. The work represents the first successful iterative synthesis of a potent CDK inhibitor based on the structure of fully activated CDK2-cyclin A. Furthermore, the potency of O(6)-cyclohexylmethyl-2-(4'- sulfamoylanilino)purine was both predicted and fully rationalized on the basis of protein-ligand interactions.

Selected figure(s)

Figure 1.
Figure 1. Inhibitor structures and binding of NU2058 to T160pCDK2 -cyclinA. a, Chemical structures of NU2058, NU6094, NU6086 and NU6102. b, T160pCDK2 -cyclinA -NU2058 structure. T160pCDK2 -cyclinA is drawn in ribbon representation. CDK2 is purple and cyclin A is gold. NU2058 bound in the CDK2 active site cleft is shown as a surface representation in green. c, CDK2 -NU2058 hydrogen bond interactions. Schematic representation of the conserved hydrogen bonds between backbone atoms of CDK2 residues Leu 83 and Glu 81, located in the hinge region, and NU2058. Hydrogen bonds are drawn as dotted lines. Arrows pointing towards Phe 80 and Lys 89 indicate the orientation of the inhibitor within the active site.

Figure 2.
Figure 2. Binding of NU6094, NU6086 and NU6102 to T160pCDK2 -cyclinA. a, T160pCDK2 -cyclinA -NU6094 structure. Selected CDK2 residues are drawn in ball-and-stick representation, with carbon atoms colored green (inhibitor) and yellow (CDK2). The final 2F[o]-F[c] electron density contoured at 0.24 e^- �-3 for NU6094 is included. Hydrogen bonds in all panels except (b) are denoted by dashed lines. b, NU6094 bound to the CDK2 active site. NU6094 is depicted as yellow CPK spheres. The CDK2 molecular surface is colored by atom type: carbon, oxygen and nitrogen atoms are green, red and blue, respectively. The figure illustrates the complementarity of the NU6094 anilino ring to the shape of the hydrophobic tunnel leading to the specificity surface. c, T160pCDK2 -cyclinA -NU6086 structure. NU6086 and selected CDK2 residues are rendered in ball-and stick-representation, with carbon atoms colored as in (a). Both conformers of the anilino ring (denoted I and II) are included. The final 2F[o]-F[c] electron density for NU6086 is contoured at 0.24 e^- �-3. d, T160pCDK2 -cyclinA -NU6102 structure. NU6102 and selected CDK2 residues are rendered in ball-and-stick representation, with carbon atoms colored as in (a). The final 2F[o]-F[c] electron density for NU6102 is contoured at 0.24 e^- �-3. e, NU6102 bound to the CDK2 active site. The CDK2 molecular surface is rendered in transparent gray so that interactions between the NU6102 sulfonamide group and the backbone nitrogen and side chain oxygen of Asp 86 are visible. Hydrogen bonds are depicted by dotted lines. NU6102 is rendered in ball and stick, with carbon atoms colored green.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 745-749) copyright 2002.

Figures were selected by an automated process.