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2V0D
Asym. Unit
Info
Asym.Unit (61 KB)
Biol.Unit 1 (53 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN CDK2 COMPLEXED WITH A THIAZOLIDINONE INHIBITOR
Authors
:
C. M. Richardson, P. Dokurno, J. B. Murray, A. E. Surgenor
Date
:
14 May 07 (Deposition) - 26 Jun 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Phosphorylation, Nucleotide-Binding, Serine/Threonine- Protein Kinase, Transferase, Atp-Binding, Cell Division, Nucleotide- Binding, Thiazolidinone Ligand, Cdk2, Kinase, Cyclin, Mitosis, Cell Cycle
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
C. M. Richardson, C. L. Nunns, D. S. Williamson, M. J. Parratt, P. Dokurno, R. Howes, J. Borgognoni, M. J. Drysdale, H. Finch, R. E. Hubbard, P. S. Jackson, P. Kierstan, G. Lentzen, J. D. Moore, J. B. Murray, H. Simmonite, A. E. Surgenor, C. J. Torrance
Discovery Of A Potent Cdk2 Inhibitor With A Novel Binding Mode, Using Virtual Screening And Initial, Structure-Guided Lead Scoping.
Bioorg. Med. Chem. Lett. V. 17 3880 2007
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: 2-IMINO-5-(1-PYRIDIN-2-YL-METH-(E)... (C53a)
2a: CHLORIDE ION (CLa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
C53
1
Ligand/Ion
2-IMINO-5-(1-PYRIDIN-2-YL-METH-(E)-YLIDENE)-1,3-THIAZOLIDIN-4-ONE
2
CL
1
Ligand/Ion
CHLORIDE ION
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:89
BINDING SITE FOR RESIDUE CL A1300
2
AC2
SOFTWARE
ILE A:10 , VAL A:18 , ALA A:31 , LYS A:33 , GLU A:81 , PHE A:82 , LEU A:83 , GLN A:131 , LEU A:134 , ALA A:144 , HOH A:2219
BINDING SITE FOR RESIDUE C53 A1299
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SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_016157 (Y15S, chain A, )
2: VAR_053927 (V18L, chain A, )
3: VAR_041972 (P45L, chain A, )
4: VAR_019988 (T290S, chain A, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_016157
Y
15
S
CDK2_HUMAN
Polymorphism
3087335
A
Y
15
S
2
UniProt
VAR_053927
V
18
L
CDK2_HUMAN
Polymorphism
11554376
A
V
18
L
3
UniProt
VAR_041972
P
45
L
CDK2_HUMAN
Unclassified
---
A
P
45
L
4
UniProt
VAR_019988
T
290
S
CDK2_HUMAN
Polymorphism
2069413
A
T
290
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:10-33)
2: PROTEIN_KINASE_ST (A:123-135)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PROTEIN_KINASE_ATP
PS00107
Protein kinases ATP-binding region signature.
CDK2_HUMAN
10-33
1
A:10-33
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
CDK2_HUMAN
123-135
1
A:123-135
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Exons
(7, 7)
Info
All Exons
Exon 1.1 (A:1-37)
Exon 1.2 (A:44-65)
Exon 1.3 (A:65-105)
Exon 1.4 (A:106-162)
Exon 1.5 (A:163-196)
Exon 1.6 (A:197-264)
Exon 1.7 (A:265-298)
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/1.6
7: Boundary 1.6/1.7
8: Boundary 1.7/-
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000266970
1
ENSE00001301614
chr12:
56360556-56360908
353
CDK2_HUMAN
1-39
39
1
A:1-37
37
1.2
ENST00000266970
2
ENSE00000838625
chr12:
56361641-56361718
78
CDK2_HUMAN
39-65
27
1
A:44-65
22
1.3
ENST00000266970
3
ENSE00000838626
chr12:
56361833-56361953
121
CDK2_HUMAN
65-105
41
1
A:65-105
41
1.4
ENST00000266970
4
ENSE00000838629
chr12:
56362562-56362732
171
CDK2_HUMAN
106-162
57
1
A:106-162
57
1.5
ENST00000266970
5
ENSE00001704611
chr12:
56363259-56363360
102
CDK2_HUMAN
163-196
34
1
A:163-196
34
1.6
ENST00000266970
6
ENSE00000938649
chr12:
56364828-56365031
204
CDK2_HUMAN
197-264
68
1
A:197-264
68
1.7
ENST00000266970
7
ENSE00001215687
chr12:
56365305-56366565
1261
CDK2_HUMAN
265-298
34
1
A:265-298
34
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2v0da_ (A:)
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(
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Protein kinase-like (PK-like)
(2589)
Superfamily
:
Protein kinase-like (PK-like)
(2589)
Family
:
Protein kinases, catalytic subunit
(1977)
Protein domain
:
Cyclin-dependent PK, CDK2
(340)
Human (Homo sapiens) [TaxId: 9606]
(336)
1a
d2v0da_
A:
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2v0dA01 (A:1-84)
2a: CATH_2v0dA02 (A:85-296)
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)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Phosphorylase Kinase; domain 1
(1392)
Homologous Superfamily
:
Phosphorylase Kinase; domain 1
(1392)
Human (Homo sapiens)
(1036)
1a
2v0dA01
A:1-84
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Transferase(Phosphotransferase); domain 1
(1379)
Homologous Superfamily
:
Transferase(Phosphotransferase) domain 1
(1379)
Human (Homo sapiens)
(1049)
2a
2v0dA02
A:85-296
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Pkinase_2v0dA01 (A:4-286)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PKinase
(934)
Family
:
Pkinase
(680)
Homo sapiens (Human)
(521)
1a
Pkinase-2v0dA01
A:4-286
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Chain A
Asymmetric Unit 1
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