Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T70176 Target Info
Target Name Cyclin-dependent kinase 2 (CDK2)
Synonyms Sin3 associated polypeptide; SIN3-associated protein; P33 protein kinase; Cell division protein kinase 2; CDKN2
Target Type Clinical trial Target
Gene Name CDK2
Biochemical Class Kinase
UniProt ID
CDK2_HUMAN
Ligand General Information  Top
Ligand Name 4-{3-[7-(4-Methylpiperazin-1-Yl)-1h-Benzimidazol-2-Yl]-1h-Indazol-6-Yl}aniline Ligand Info
Canonical SMILES CN1CCN(CC1)C2=CC=CC3=C2N=C(N3)C4=NNC5=C4C=CC(=C5)C6=CC=C(C=C6)N
InChI 1S/C25H25N7/c1-31-11-13-32(14-12-31)22-4-2-3-20-24(22)28-25(27-20)23-19-10-7-17(15-21(19)29-30-23)16-5-8-18(26)9-6-16/h2-10,15H,11-14,26H2,1H3,(H,27,28)(H,29,30)
InChIKey LPSCCOBGZSKECZ-UHFFFAOYSA-N
PubChem Compound ID 135566451
Drug Binding Sites of Target  Top
PDB ID: 3F5X      CDK-2-Cyclin complex with indazole inhibitor 9 bound at its active site
Method X-ray diffraction Resolution 2.40 Å Mutation No [1]
PDB Sequence
MENFQKVEKI
10
GEGTYGVVYK
20
ARNKLTGEVV
30
ALKKIRLDTE
40
TEGVPSTAIR
50

EISLLKELNH
60
PNIVKLLDVI
70
HTENKLYLVF
80
EFLHQDLKKF
90
MDASALTGIP
100

LPLIKSYLFQ
110
LLQGLAFCHS
120
HRVLHRDLKP
130
QNLLINTEGA
140
IKLADFGLAR
150

AFGVPVRTYT
160
HEVVTLWYRA
170
PEILLGCKYY
180
STAVDIWSLG
190
CIFAEMVTRR
200

ALFPGDSEID
210
QLFRIFRTLG
220
TPDEVVWPGV
230
TSMPDYKPSF
240
PKWARQDFSK
250

VVPPLDEDGR
260
SLLSQMLHYD
270
PKRISAKAAL
281
AHPFFQDVTK
291
PVPHLRL
Residue
Distance (Å)
ILE10
3.266
GLY11
4.770
VAL18
4.285
ALA31
3.404
LYS33
2.838
GLU51
2.342
LEU55
3.590
VAL64
3.791
PHE80
3.312
GLU81
2.843
PHE82
3.438
Residue
Distance (Å)
LEU83
2.708
HIS84
3.107
GLN85
4.042
ASP86
2.804
LYS89
3.305
GLN131
3.779
LEU134
3.362
ALA144
3.693
ASP145
3.334
PHE146
3.041
GLY147
4.571
PDB ID: 3EZV      CDK-2 with indazole inhibitor 9 bound at its active site
Method X-ray diffraction Resolution 1.99 Å Mutation No [1]
PDB Sequence
MENFQKVEKI
10
GEGTYGVVYK
20
ARNKLTGEVV
30
ALKKIRVPST
47
AIREISLLKE
57

LNHPNIVKLL
67
DVIHTENKLY
77
LVFEFLHQDL
87
KKFMDASALT
97
GIPLPLIKSY
107

LFQLLQGLAF
117
CHSHRVLHRD
127
LKPQNLLINT
137
EGAIKLADFG
147
LVVTLWYRAP
171

EILLGCKYYS
181
TAVDIWSLGC
191
IFAEMVTRRA
201
LFPGDSEIDQ
211
LFRIFRTLGT
221

PDEVVWPGVT
231
SMPDYKPSFP
241
KWARQDFSKV
251
VPPLDEDGRS
261
LLSQMLHYDP
271

NKRISAKAAL
281
AHPFFQDVTK
291
PVPHLRL
Residue
Distance (Å)
ILE10
3.443
VAL18
4.381
ALA31
3.290
LYS33
3.850
VAL64
3.848
PHE80
2.983
GLU81
2.758
PHE82
3.612
LEU83
2.528
Residue
Distance (Å)
HIS84
3.337
GLN85
3.935
ASP86
3.285
GLN131
3.577
LEU134
3.299
ALA144
3.663
ASP145
3.056
PHE146
3.434
References  Top
REF 1 2-(6-Phenyl-1H-indazol-3-yl)-1H-benzo[d]imidazoles: design and synthesis of a potent and isoform selective PKC-zeta inhibitor. Bioorg Med Chem Lett. 2009 Feb 1;19(3):908-11.

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