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2UZD
Biol. Unit 1
Info
Asym.Unit (194 KB)
Biol.Unit 1 (94 KB)
Biol.Unit 2 (95 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
:
27 Apr 07 (Deposition) - 26 Jun 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.72
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Transferase, Atp-Binding, Phosphorylation, Cdk2, Kinase, Cyclin, Mitosis, Cell Cycle, Cell Division, Nucleotide- Binding, Serine/Threonine-Protein Kinase, Thiazolidinone Ligand
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
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: 4-{5-[(Z)-(2-IMINO-4-OXO-1,3-THIAZ... (C85a)
1b: 4-{5-[(Z)-(2-IMINO-4-OXO-1,3-THIAZ... (C85b)
2a: PHOSPHOTHREONINE (TPOa)
2b: PHOSPHOTHREONINE (TPOb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
C85
1
Ligand/Ion
4-{5-[(Z)-(2-IMINO-4-OXO-1,3-THIAZOLIDIN-5-YLIDENE)METHYL]FURAN-2-YL}BENZENESULFONAMIDE
2
TPO
1
Mod. Amino Acid
PHOSPHOTHREONINE
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ILE A:10 , ALA A:31 , PHE A:80 , LEU A:83 , HIS A:84 , GLN A:85 , ASP A:86 , LYS A:89 , LEU A:134 , ASP A:145 , HOH A:2053
BINDING SITE FOR RESIDUE C85 A1297
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SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are only available for the asymmetric unit)
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
(3, 3)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:10-33)
2: PROTEIN_KINASE_ST (A:123-135)
3: CYCLINS (B:211-242)
;
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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
-
3
CYCLINS
PS00292
Cyclins signature.
CCNA2_HUMAN
211-242
1
B:211-242
-
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Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d2uzdb1 (B:175-309)
1b: SCOP_d2uzdb2 (B:310-432)
1c: SCOP_d2uzdd1 (D:175-309)
1d: SCOP_d2uzdd2 (D:310-432)
2a: SCOP_d2uzda_ (A:)
2b: SCOP_d2uzdc_ (C:)
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)
Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cyclin-like
(137)
Superfamily
:
Cyclin-like
(137)
Family
:
Cyclin
(117)
Protein domain
:
Cyclin A
(82)
Human (Homo sapiens) [TaxId: 9606]
(73)
1a
d2uzdb1
B:175-309
1b
d2uzdb2
B:310-432
1c
d2uzdd1
D:175-309
1d
d2uzdd2
D:310-432
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)
2a
d2uzda_
A:
2b
d2uzdc_
C:
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CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_2uzdA01 (A:1-84)
1b: CATH_2uzdC01 (C:1-84)
2a: CATH_2uzdB01 (B:181-194,B:308-432)
2b: CATH_2uzdB02 (B:195-307)
2c: CATH_2uzdD02 (D:195-307)
2d: CATH_2uzdD01 (D:181-194,D:308-432)
3a: CATH_2uzdA02 (A:85-296)
3b: CATH_2uzdC02 (C:85-296)
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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
2uzdA01
A:1-84
1b
2uzdC01
C:1-84
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cyclin A; domain 1
(136)
Homologous Superfamily
:
[code=1.10.472.10, no name defined]
(99)
Human (Homo sapiens)
(84)
2a
2uzdB01
B:181-194,B:308-432
2b
2uzdB02
B:195-307
2c
2uzdD02
D:195-307
2d
2uzdD01
D:181-194,D:308-432
Topology
:
Transferase(Phosphotransferase); domain 1
(1379)
Homologous Superfamily
:
Transferase(Phosphotransferase) domain 1
(1379)
Human (Homo sapiens)
(1049)
3a
2uzdA02
A:85-296
3b
2uzdC02
C:85-296
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Cyclin_C_2uzdD01 (D:309-427)
1b: PFAM_Cyclin_C_2uzdD02 (D:309-427)
2a: PFAM_Cyclin_N_2uzdD03 (D:181-307)
2b: PFAM_Cyclin_N_2uzdD04 (D:181-307)
3a: PFAM_Pkinase_2uzdC01 (C:4-286)
3b: PFAM_Pkinase_2uzdC02 (C:4-286)
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)
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)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
Cyclin
(63)
Family
:
Cyclin_C
(40)
Homo sapiens (Human)
(36)
1a
Cyclin_C-2uzdD01
D:309-427
1b
Cyclin_C-2uzdD02
D:309-427
Family
:
Cyclin_N
(51)
Homo sapiens (Human)
(43)
2a
Cyclin_N-2uzdD03
D:181-307
2b
Cyclin_N-2uzdD04
D:181-307
Clan
:
PKinase
(934)
Family
:
Pkinase
(680)
Homo sapiens (Human)
(521)
3a
Pkinase-2uzdC01
C:4-286
3b
Pkinase-2uzdC02
C:4-286
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Asym.Unit (194 KB)
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