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 3-[({3-Ethyl-5-[(2s)-2-(2-Hydroxyethyl)piperidin-1-Yl]pyrazolo[1,5-A]pyrimidin-7-Yl}amino)methyl]-1-Hydroxypyridinium Ligand Info
Canonical SMILES CCC1=C2N=C(C=C(N2N=C1)NCC3=C[N+](=CC=C3)O)N4CCCCC4CCO
InChI 1S/C21H29N6O2/c1-2-17-14-23-27-19(22-13-16-6-5-9-25(29)15-16)12-20(24-21(17)27)26-10-4-3-7-18(26)8-11-28/h5-6,9,12,14-15,18,22,28-29H,2-4,7-8,10-11,13H2,1H3/q+1/t18-/m0/s1
InChIKey WBUFFOKXERTKGU-SFHVURJKSA-N
PubChem Compound ID 135211563
Drug Binding Sites of Target  Top
PDB ID: 4KD1      CDK2 in complex with Dinaciclib
Method X-ray diffraction Resolution 1.70 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
PNKRISAKAA
280
LAHPFFQDVT
290
KPVPHLRL
Residue
Distance (Å)
GLU8
4.295
ILE10
3.406
GLY11
3.923
GLU12
3.811
GLY13
4.256
VAL18
3.635
ALA31
3.305
LYS33
2.565
VAL64
3.928
PHE80
3.584
GLU81
3.200
Residue
Distance (Å)
PHE82
3.655
LEU83
2.650
HIS84
3.655
GLN85
3.326
ASP86
3.579
LYS89
2.986
GLN131
3.655
ASN132
4.090
LEU134
3.477
ALA144
3.835
ASP145
4.377
PDB ID: 5L2W      The X-ray co-crystal structure of human CDK2/CyclinE and Dinaciclib.
Method X-ray diffraction Resolution 2.80 Å Mutation No [2]
PDB Sequence
SMENFQKVEK
9
IGEGTYGVVY
19
KARNKLTGEV
29
VALKKIRLDT
39
ETEGVPSTAI
49

REISLLKELN
59
HPNIVKLLDV
69
IHTENKLYLV
79
FEFLHQDLKK
89
FMDASALTGI
99

PLPLIKSYLF
109
QLLQGLAFCH
119
SHRVLHRDLK
129
PQNLLINTEG
139
AIKLADFGLA
149

RAFGVPVRTY
159
HEVVTLWYRA
170
PEILLGCKYY
180
STAVDIWSLG
190
CIFAEMVTRR
200

ALFPGDSEID
210
QLFRIFRTLG
220
TPDEVVWPGV
230
TSMPDYKPSF
240
PKWARQDFSK
250

VVPPLDEDGR
260
SLLSQMLHYD
270
PNKRISAKAA
280
LAHPFFQDVT
290
KPVPHLR
Residue
Distance (Å)
GLU8
4.154
ILE10
3.401
GLY11
4.203
GLU12
3.963
GLY13
3.782
VAL18
3.775
ALA31
3.376
VAL64
4.295
PHE80
3.527
GLU81
3.348
PHE82
3.414
Residue
Distance (Å)
LEU83
2.722
HIS84
3.650
GLN85
3.498
ASP86
3.803
LYS89
3.507
GLN131
3.705
ASN132
3.831
LEU134
3.392
ALA144
3.600
ASP145
3.768
References  Top
REF 1 Cyclin-dependent kinase inhibitor dinaciclib interacts with the acetyl-lysine recognition site of bromodomains. ACS Chem Biol. 2013 Nov 15;8(11):2360-5.
REF 2 Spectrum and Degree of CDK Drug Interactions Predicts Clinical Performance. Mol Cancer Ther. 2016 Oct;15(10):2273-2281.

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