Version: 3.2
Updated: 29-Oct-2025
Cyclin-dependent kinase 2
Kinase structure
Kinase:CDK2
Family:CDK
Group:CMGC
Species:HUMAN
IUPHAR/BPS ID:1973
PDB:5D1J
sc-PDB:
KIDFamMap:Search
Release date:2015-08-12
PubMed: 15027863
Chain:A
Orthosteric ligand:56H
2D structure of the orthosteric ligand
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The orthosteric binding pocket
Structural information
DFG conformation:in
αC-helix conformation:out
G-rich loop angle (distance):-
G-rich loop rotation:-
Quality Score:4.8
Resolution:1.8 Å
Missing Residues:8
Missing Atoms:23
Ligand binding mode
PocketsSubpocketsWaters
front
Cluster
I2
I5
Ligand
No
No
Protein
Yes
Yes

Pocket alignment
Uniprot sequence:EKIGEGTYGVVYKVALKKITAIREISLLKELNPNIVKLLDVYLVFEFLH-QDLKKFMDAFCHSHRVLHRDLKPQNLLILADFGLA
Sequence structure:EKIGE__YGVVYKVALKK___IREISLLKELNPNIVKLLDVYLVFEFLH_QDLKKFMDAFCHSHRVLHRDLKPQNLLILADF___

Ligand affinity
ChEMBL ID:CHEMBL296468
Bioaffinities: 150 records for 79 kinases
Species Kinase (ChEMBL naming) Median Min Max Type Records
Homo sapiensAMP-activated protein kinase, alpha-1 subunit5.15.15.1pKd1
Homo sapiensBR serine/threonine-protein kinase 25.35.35.3pKd1
Homo sapiensCasein kinase I alpha666pKd1
Homo sapiensCasein kinase I delta5.85.85.8pKd2
Homo sapiensCasein kinase I epsilon666pKd2
Homo sapiensCell division cycle 2-like protein kinase 6666pKd2
Homo sapiensCell division protein kinase 85.95.95.9pKd2
Homo sapiensCell division protein kinase 86.76.76.7pKi1
Homo sapiensCitron Rho-interacting kinase5.45.45.4pKd1
Homo sapiensc-Jun N-terminal kinase 35.25.25.2pKd1
Homo sapiensCyclin-dependent kinase 16.36.36.3pKi1
Homo sapiensCyclin-dependent kinase 27.37.37.4pIC503
Homo sapiensCyclin-dependent kinase 27.27.27.2pKd2
Homo sapiensCyclin-dependent kinase 27.47.47.4pKi1
Homo sapiensCyclin-dependent kinase 37.37.37.3pKd2
Homo sapiensCyclin-dependent kinase 47.27.27.2pKd2
Homo sapiensCyclin-dependent kinase 4666pKi1
Homo sapiensCyclin-dependent kinase 56.16.16.1pKd2
Homo sapiensCyclin-dependent kinase 57.37.37.3pKi1
Homo sapiensCyclin-dependent kinase 77.57.57.5pKd2
Homo sapiensCyclin-dependent kinase 76.96.96.9pKi1
Homo sapiensCyclin-dependent kinase 96.36.38.4pIC503
Homo sapiensCyclin-dependent kinase 97.17.17.1pKd2
Homo sapiensCyclin-dependent kinase 9888.4pKi2
Homo sapiensCyclin-dependent kinase-like 27.47.47.4pKd1
Homo sapiensCyclin-dependent kinase-like 35.95.95.9pKd1
Homo sapiensCyclin-dependent kinase-like 58.88.88.8pKd1
Homo sapiensDual specificity protein kinase CLK2666pKd2
Homo sapiensDual specificity protein kinase CLK46.16.16.1pKd2
Homo sapiensDual specificity protein kinase CLK46.46.46.4pKi1
Homo sapiensDual-specificity tyrosine-phosphorylation regulated kinase 1A6.56.56.5pKd1
Homo sapiensDual-specificity tyrosine-phosphorylation regulated kinase 1A5.85.85.8pKi1
Homo sapiensDual specificity tyrosine-phosphorylation-regulated kinase 1B6.76.76.7pKd2
Homo sapiensDual specificity tyrosine-phosphorylation-regulated kinase 1B6.66.66.6pKi1
Homo sapiensDual-specificity tyrosine-phosphorylation regulated kinase 25.85.85.8pKd1
Homo sapiensDual specificty protein kinase CLK16.46.46.4pKd2
Homo sapiensGlycogen synthase kinase-3 alpha7.67.67.6pKd2
Homo sapiensGlycogen synthase kinase-3 alpha6.96.96.9pKi1
Homo sapiensGlycogen synthase kinase-3 beta7.47.47.4pKd2
Homo sapiensGlycogen synthase kinase-3 beta6.66.66.6pKi1
Homo sapiensHomeodomain-interacting protein kinase 15.85.85.8pKd1
Homo sapiensHomeodomain-interacting protein kinase 25.85.85.8pKd1
Homo sapiensHomeodomain-interacting protein kinase 35.75.75.7pKd1
Homo sapiensInterleukin-1 receptor-associated kinase 35.55.55.5pKd2
Homo sapiensMAP kinase-interacting serine/threonine-protein kinase MNK15.45.45.4pKd2
Homo sapiensMAP kinase signal-integrating kinase 25.45.45.4pKd1
Homo sapiensMaternal embryonic leucine zipper kinase5.35.35.3pKd2
Homo sapiensMaternal embryonic leucine zipper kinase6.86.86.8pKi1
Homo sapiensMicrotubule-associated serine/threonine-protein kinase 15.25.25.2pKd1
Homo sapiensMitogen-activated protein kinase 156.96.96.9pKd2
Homo sapiensMitogen-activated protein kinase 45.45.45.4pKd2
Homo sapiensMitogen-activated protein kinase 66.36.36.3pKd2
Homo sapiensMitogen-activated protein kinase 76.26.26.2pKd2
Homo sapiensMitogen-activated protein kinase kinase kinase 75.95.95.9pKd1
Homo sapiensMyosin light chain kinase5.85.85.8pKd1
Homo sapiensmyosin light chain kinase 2666pKd2
Homo sapiensMyosin light chain kinase family member 45.65.65.6pKd1
Gallus gallusMyosin light chain kinase, smooth muscle5.85.85.8pKd1
Homo sapiensNUAK family SNF1-like kinase 25.85.85.8pKd2
Homo sapiensPhosphorylase kinase gamma subunit 15.45.45.4pKd2
Homo sapiensPhosphorylase kinase gamma subunit 26.36.36.3pKd1
Homo sapiensPITSLRE serine/threonine-protein kinase CDC2L1777pKd2
Homo sapiensPITSLRE serine/threonine-protein kinase CDC2L27.37.37.3pKd2
Homo sapiensProtein kinase C mu5.95.95.9pKd2
Homo sapiensProtein kinase C nu6.16.16.1pKd2
Homo sapiensProtein kinase C nu5.85.85.8pKi1
Homo sapiensRibosomal protein S6 kinase alpha 55.15.15.1pKd2
Homo sapiensSerine/threonine-protein kinase 17A6.46.46.4pKd2
Homo sapiensSerine/threonine-protein kinase 366.66.66.6pKd2
Homo sapiensSerine/threonine-protein kinase Aurora-A5.15.15.1pKd2
Homo sapiensSerine/threonine-protein kinase Aurora-C5.35.35.3pKd1
Homo sapiensSerine/threonine-protein kinase B-raf5.85.85.9pKd2
Homo sapiensSerine/threonine-protein kinase D25.45.45.4pKd2
Homo sapiensSerine/threonine-protein kinase DCLK15.85.85.8pKd2
Homo sapiensSerine/threonine-protein kinase DCLK2666pKd2
Homo sapiensSerine/threonine-protein kinase DCLK35.85.85.8pKd2
Homo sapiensSerine/threonine-protein kinase GAK5.85.85.8pKd2
Homo sapiensSerine/threonine-protein kinase ICK6.86.86.8pKd1
Homo sapiensSerine/threonine-protein kinase MAK5.65.65.6pKd1
Homo sapiensSerine/threonine-protein kinase PAK 35.55.55.5pKd2
Homo sapiensSerine/threonine-protein kinase PCTAIRE-18.28.28.2pKd2
Homo sapiensSerine/threonine-protein kinase PCTAIRE-27.97.97.9pKd2
Homo sapiensSerine/threonine-protein kinase PCTAIRE-37.47.47.4pKd2
Homo sapiensSerine/threonine-protein kinase PFTAIRE-16.26.26.2pKd2
Homo sapiensSerine/threonine-protein kinase PFTAIRE-26.16.16.1pKd1
Homo sapiensSerine/threonine-protein kinase RIO25.85.85.8pKd1
Homo sapiensSerine/threonine-protein kinase TAO15.95.95.9pKd1
Homo sapiensSerine/threonine-protein kinase TAO16.16.16.1pKi1
Homo sapiensSerine/threonine-protein kinase TAO25.85.85.8pKd1
Homo sapiensSerine/threonine-protein kinase TAO36.26.26.2pKd1
Homo sapiensSerine/threonine-protein kinase ULK15.65.65.6pKd1
Homo sapiensTGF-beta receptor type II5.65.65.6pKd2
Homo sapiensTyrosine-protein kinase receptor FLT35.155.5pKd5
Homo sapiensUncharacterized aarF domain-containing protein kinase 45.55.55.5pKd1
Homo sapiensVascular endothelial growth factor receptor 1555pKd1


Kinase-ligand interaction pattern
• Hydrophobic • Aromatic face-to-face • Aromatic face-to-edge • H-bond donor • H-bond acceptor • Ionic positive • Ionic negative
I g.l II III αC
1 E
8		2 K
9		3 I
10		4 G
11		5 E
12		6 _
_		7 _
_		8 Y
15		9 G
16		10 V
17		11 V
18		12 Y
19		13 K
20		14 V
30		15 A
31		16 L
32		17 K
33		18 K
34		19 _
_		20 _
_
••••••
αC b.l IV
21 _
_		22 I
35		23 R
50		24 E
51		25 I
52		26 S
53		27 L
54		28 L
55		29 K
56		30 E
57		31 L
58		32 N
59		33 P
61		34 N
62		35 I
63		36 V
64		37 K
65		38 L
66		39 L
67		40 D
68
•
IV V GK hinge linker αD αE
41 V
69		42 Y
77		43 L
78		44 V
79		45 F
80		46 E
81		47 F
82		48 L
83		49 H
84		50 _
_		51 Q
85		52 D
86		53 L
87		54 K
88		55 K
89		56 F
90		57 M
91		58 D
92		59 A
93		60 F
117
•••••••••
αE VI c.l VII VIII x
61 C
118		62 H
119		63 S
120		64 H
121		65 R
122		66 V
123		67 L
124		68 H
125		69 R
126		70 D
127		71 L
128		72 K
129		73 P
130		74 Q
131		75 N
132		76 L
133		77 L
134		78 I
135		79 L
143		80 A
144
••••
DFG a.l
81 D
145		82 F
146		83 _
_		84 _
_		85 _
_
•

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