PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4BCO
Asym. Unit
Info
Asym.Unit (383 KB)
Biol.Unit 1 (195 KB)
Biol.Unit 2 (185 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF CDK2 IN COMPLEX WITH CYCLIN A AND A 2-AMINO-4-HETEROARYL-PYRIMIDINE INHIBITOR
Authors
:
A. J. Hole, S. Baumli, S. Wang, J. A. Endicott, M. E. M. Noble
Date
:
02 Oct 12 (Deposition) - 09 Jan 13 (Release) - 27 Feb 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Transferase-Cell Cycle Complex, Cdk-Cyclin Complex, Cyclin-Inhibitor, Structure-Based Drug Design
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. J. Hole, S. Baumli, H. Shao, S. Shi, C. Pepper, P. M. Fischer, S. Wang, J. A. Endicott, M. E. M. Noble
Comparative Structural And Functional Studies Of 4-(Thiazol- 5-Yl)-2-(Phenylamino)Pyrimidine-5-Carbonitrile Cdk9 Inhibitors Suggest The Basis For Isotype Selectivity.
J. Med. Chem. V. 56 660 2013
[
close entry info
]
Hetero Components
(4, 10)
Info
All Hetero Components
1a: MONOTHIOGLYCEROL (SGMa)
1b: MONOTHIOGLYCEROL (SGMb)
1c: MONOTHIOGLYCEROL (SGMc)
1d: MONOTHIOGLYCEROL (SGMd)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
3a: 2-[[3-(4-ETHANOYL-1,4-DIAZEPAN-1-Y... (T6Qa)
3b: 2-[[3-(4-ETHANOYL-1,4-DIAZEPAN-1-Y... (T6Qb)
4a: PHOSPHOTHREONINE (TPOa)
4b: PHOSPHOTHREONINE (TPOb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SGM
4
Ligand/Ion
MONOTHIOGLYCEROL
2
SO4
2
Ligand/Ion
SULFATE ION
3
T6Q
2
Ligand/Ion
2-[[3-(4-ETHANOYL-1,4-DIAZEPAN-1-YL)PHENYL]AMINO]-4-[4-METHYL-2-(METHYLAMINO)-1,3-THIAZOL-5-YL]PYRIMIDINE-5-CARBONITRILE
4
TPO
2
Mod. Amino Acid
PHOSPHOTHREONINE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:8 , GLY A:13 , LYS A:20 , ALA A:31 , VAL A:64 , PHE A:80 , GLU A:81 , PHE A:82 , LEU A:83 , HIS A:84 , GLN A:85 , LYS A:89 , ASN A:132 , LEU A:134 , ASP A:145 , HOH A:2039
BINDING SITE FOR RESIDUE T6Q A1299
2
AC2
SOFTWARE
GLU C:8 , GLY C:13 , VAL C:18 , VAL C:64 , PHE C:80 , GLU C:81 , PHE C:82 , LEU C:83 , HIS C:84 , ASP C:86 , ASN C:132 , LEU C:134 , ASP C:145 , HOH C:2056 , GLN D:403
BINDING SITE FOR RESIDUE T6Q C1298
3
AC3
SOFTWARE
CYS B:327 , GLU B:330
BINDING SITE FOR RESIDUE SGM B1433
4
AC4
SOFTWARE
HOH A:2048 , MET B:189 , LYS B:192 , CYS B:193 , ARG B:241 , ASP B:305 , HOH B:2092
BINDING SITE FOR RESIDUE SGM B1434
5
AC5
SOFTWARE
MET D:189 , LYS D:192 , CYS D:193 , ARG D:241 , ASP D:305 , ALA D:308
BINDING SITE FOR RESIDUE SGM D1433
6
AC6
SOFTWARE
ASN D:326 , CYS D:327 , GLU D:330
BINDING SITE FOR RESIDUE SGM D1434
7
AC7
SOFTWARE
LYS B:202 , GLN B:203 , LEU B:243 , SER B:244 , SER B:245 , MET B:246 , SER B:247 , HOH B:2072
BINDING SITE FOR RESIDUE SO4 B1435
8
AC8
SOFTWARE
LYS A:65 , LYS D:202 , LEU D:243 , SER D:245 , MET D:246 , SER D:247
BINDING SITE FOR RESIDUE SO4 D1435
[
close Site info
]
SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_016157 (Y15S, chain A/C, )
2: VAR_053927 (V18L, chain A/C, )
3: VAR_041972 (P45L, chain A/C, )
4: VAR_019988 (T290S, chain A/C, )
View:
Select:
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/C
Y
15
S
2
UniProt
VAR_053927
V
18
L
CDK2_HUMAN
Polymorphism
11554376
A/C
V
18
L
3
UniProt
VAR_041972
P
45
L
CDK2_HUMAN
Unclassified
---
A/C
P
45
L
4
UniProt
VAR_019988
T
290
S
CDK2_HUMAN
Polymorphism
2069413
A/C
T
290
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:10-33,C:10-33)
2: PROTEIN_KINASE_ST (A:123-135,C:123-135)
3: CYCLINS (B:211-242,D:211-242)
;
View:
Select:
Label:
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
2
A:10-33
C:10-33
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
CDK2_HUMAN
123-135
2
A:123-135
C:123-135
3
CYCLINS
PS00292
Cyclins signature.
CCNA2_BOVIN
209-240
2
B:211-242
D:211-242
[
close PROSITE info
]
Exons
(7, 14)
Info
All Exons
Exon 1.1 (A:1-39 | C:1-39)
Exon 1.2 (A:39-65 | C:39-65)
Exon 1.3 (A:65-105 | C:65-105)
Exon 1.4 (A:106-162 | C:106-162)
Exon 1.5 (A:163-196 | C:163-196)
Exon 1.6 (A:197-264 | C:197-264 (gaps))
Exon 1.7 (A:265-298 | C:265-296)
View:
Select:
Label:
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/-
View:
Label:
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
2
A:1-39
C:1-39
39
39
1.2
ENST00000266970
2
ENSE00000838625
chr12:
56361641-56361718
78
CDK2_HUMAN
39-65
27
2
A:39-65
C:39-65
27
27
1.3
ENST00000266970
3
ENSE00000838626
chr12:
56361833-56361953
121
CDK2_HUMAN
65-105
41
2
A:65-105
C:65-105
41
41
1.4
ENST00000266970
4
ENSE00000838629
chr12:
56362562-56362732
171
CDK2_HUMAN
106-162
57
2
A:106-162
C:106-162
57
57
1.5
ENST00000266970
5
ENSE00001704611
chr12:
56363259-56363360
102
CDK2_HUMAN
163-196
34
2
A:163-196
C:163-196
34
34
1.6
ENST00000266970
6
ENSE00000938649
chr12:
56364828-56365031
204
CDK2_HUMAN
197-264
68
2
A:197-264
C:197-264 (gaps)
68
68
1.7
ENST00000266970
7
ENSE00001215687
chr12:
56365305-56366565
1261
CDK2_HUMAN
265-298
34
2
A:265-298
C:265-296
34
32
[
close EXON info
]
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d4bcob1 (B:175-308)
1b: SCOP_d4bcob2 (B:309-432)
1c: SCOP_d4bcod1 (D:177-308)
1d: SCOP_d4bcod2 (D:309-432)
2a: SCOP_d4bcoa_ (A:)
2b: SCOP_d4bcoc_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cyclin-like
(137)
Superfamily
:
Cyclin-like
(137)
Family
:
Cyclin
(117)
Protein domain
:
automated matches
(10)
Cow (Bos taurus) [TaxId: 9913]
(3)
1a
d4bcob1
B:175-308
1b
d4bcob2
B:309-432
1c
d4bcod1
D:177-308
1d
d4bcod2
D:309-432
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
d4bcoa_
A:
2b
d4bcoc_
C:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (383 KB)
Header - Asym.Unit
Biol.Unit 1 (195 KB)
Header - Biol.Unit 1
Biol.Unit 2 (185 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
4BCO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help