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 T89361 Target Info
Target Name Cyclin-dependent kinase 6 (CDK6)
Synonyms Serine/threonine-protein kinase PLSTIRE; Serine/threonine protein kinase PLSTIRE; Cell division protein kinase 6; CDKN6
Target Type Successful Target
Gene Name CDK6
Biochemical Class Kinase
UniProt ID
CDK6_HUMAN
Ligand General Information  Top
Ligand Name Palbociclib Ligand Info
Canonical SMILES CC1=C(C(=O)N(C2=NC(=NC=C12)NC3=NC=C(C=C3)N4CCNCC4)C5CCCC5)C(=O)C
InChI 1S/C24H29N7O2/c1-15-19-14-27-24(28-20-8-7-18(13-26-20)30-11-9-25-10-12-30)29-22(19)31(17-5-3-4-6-17)23(33)21(15)16(2)32/h7-8,13-14,17,25H,3-6,9-12H2,1-2H3,(H,26,27,28,29)
InChIKey AHJRHEGDXFFMBM-UHFFFAOYSA-N
PubChem Compound ID 5330286
Drug Binding Sites of Target  Top
PDB ID: 2EUF      X-ray structure of human CDK6-Vcyclin in complex with the inhibitor PD0332991
Method X-ray diffraction Resolution 3.00 Å Mutation No [1]
PDB Sequence
DQQYECVAEI
19
GEGAYGKVFK
29
ARDLKNGGRF
39
VALKRVRVQT
49
GEEGMPLSTI
59

REVAVLRHLE
69
TFEHPNVVRL
79
FDVCTVSRTD
89
RETKLTLVFE
99
HVDQDLTTYL
109

DKVPEPGVPT
119
ETIKDMMFQL
129
LRGLDFLHSH
139
RVVHRDLKPQ
149
NILVTSSGQI
159

KLADFGLARI
169
YSFQMALTSV
179
VVTLWYRAPE
189
VLLQSSYATP
199
VDLWSVGCIF
209

AEMFRRKPLF
219
RGSSDVDQLG
229
KILDVIGLPG
239
EEDWPAQPIE
263
KFVTDIDELG
273

KDLLLKCLTF
283
NPAKRISAYS
293
ALSHPYFQDL
303
ER
Residue
Distance (Å)
ILE19
3.420
GLY20
3.834
GLU21
4.527
GLY22
4.235
VAL27
3.972
ALA41
4.052
LYS43
3.831
GLU61
4.232
VAL77
3.084
PHE98
3.288
GLU99
3.637
HIS100
4.198
Residue
Distance (Å)
VAL101
2.716
ASP102
3.382
GLN103
3.466
ASP104
3.717
THR107
3.049
GLN149
3.210
ASN150
3.831
LEU152
3.271
ALA162
3.426
ASP163
2.710
PHE164
4.626
PDB ID: 5L2I      The X-ray co-crystal structure of human CDK6 and Palbociclib.
Method X-ray diffraction Resolution 2.75 Å Mutation No [2]
PDB Sequence
DQQYECVAEI
19
GEGAYGKVFK
29
ARDLKNGGRF
39
VALKRVRPLS
57
TIREVAVLRH
67

LETFEHPNVV
77
RLFDVCTKLT
95
LVFEHVDQDL
105
TTYLDKVPEP
115
GVPTETIKDM
125

MFQLLRGLDF
135
LHSHRVVHRD
145
LKPQNILVTS
155
SGQIKLADFG
165
LVTLWYRAPE
189

VLLQSSYATP
199
VDLWSVGCIF
209
AEMFRRKPLF
219
RGSSDVDQLG
229
KILDVIGLPG
239

EEDWPRDVAL
249
PRQAFKSAQP
261
IEKFVTDIDE
271
LGKDLLLKCL
281
TFNPAKRISA
291

YSALSHPYFQ
301
Residue
Distance (Å)
GLU18
4.197
ILE19
2.670
GLY20
3.575
TYR24
2.805
VAL27
2.493
ALA41
3.090
LYS43
3.867
VAL77
3.258
PHE98
2.948
GLU99
2.392
HIS100
3.550
Residue
Distance (Å)
VAL101
1.960
ASP102
3.968
GLN103
3.355
ASP104
2.993
THR107
2.769
GLN149
2.564
ASN150
3.049
LEU152
2.643
ALA162
3.584
ASP163
3.060
PHE164
4.923
References  Top
REF 1 Toward understanding the structural basis of cyclin-dependent kinase 6 specific inhibition. J Med Chem. 2006 Jun 29;49(13):3826-31.
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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