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2X7O
Asym. Unit
Info
Asym.Unit (280 KB)
Biol.Unit 1 (58 KB)
Biol.Unit 2 (58 KB)
Biol.Unit 3 (58 KB)
Biol.Unit 4 (58 KB)
Biol.Unit 5 (58 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF TGFBRI COMPLEXED WITH AN INDOLINONE INHIBITOR
Authors
:
G. J. Roth, A. Heckel, T. Brandl, M. Grauert, S. Hoerer, J. T. Kley, G. Sch P. Baum, D. Mennerich, A. Schnapp, J. E. Park
Date
:
03 Mar 10 (Deposition) - 20 Oct 10 (Release) - 25 May 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.70
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Keywords
:
Kinase, Transferase, Glycoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. J. Roth, A. Heckel, T. Brandl, M. Grauert, S. Hoerer, J. T. Kley, G. Schnapp, P. Baum, D. Mennerich, A. Schnapp, J. E. Park
Design, Synthesis And Evaluation Of Indolinones As Inhibitors Of The Transforming Growth Factor Beta Receptor I (Tgfbri)
J. Med. Chem. V. 53 7287 2010
[
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Hetero Components
(1, 5)
Info
All Hetero Components
1a: (3Z)-N-ETHYL-N-METHYL-2-OXO-3-(PHE... (ZOPa)
1b: (3Z)-N-ETHYL-N-METHYL-2-OXO-3-(PHE... (ZOPb)
1c: (3Z)-N-ETHYL-N-METHYL-2-OXO-3-(PHE... (ZOPc)
1d: (3Z)-N-ETHYL-N-METHYL-2-OXO-3-(PHE... (ZOPd)
1e: (3Z)-N-ETHYL-N-METHYL-2-OXO-3-(PHE... (ZOPe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ZOP
5
Ligand/Ion
(3Z)-N-ETHYL-N-METHYL-2-OXO-3-(PHENYL{[4-(PIPERIDIN-1-YLMETHYL)PHENYL]AMINO}METHYLIDENE)-2,3-DIHYDRO-1H-INDOLE-6-CARBOXAMIDE
[
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]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ILE A:211 , GLY A:212 , VAL A:219 , ALA A:230 , LYS A:232 , GLU A:245 , LEU A:260 , LEU A:278 , SER A:280 , ASP A:281 , HIS A:283 , GLU A:284 , HIS A:285 , GLY A:286 , ASP A:290 , ARG A:294 , LEU A:340
BINDING SITE FOR RESIDUE ZOP A 600
2
AC2
SOFTWARE
ILE B:211 , VAL B:219 , ALA B:230 , LYS B:232 , GLU B:245 , LEU B:260 , LEU B:278 , SER B:280 , ASP B:281 , TYR B:282 , HIS B:283 , GLU B:284 , GLY B:286 , ASP B:290 , ARG B:294 , LEU B:340
BINDING SITE FOR RESIDUE ZOP B 600
3
AC3
SOFTWARE
ILE C:211 , GLY C:212 , VAL C:219 , ALA C:230 , LYS C:232 , GLU C:245 , LEU C:260 , LEU C:278 , SER C:280 , ASP C:281 , TYR C:282 , HIS C:283 , GLU C:284 , HIS C:285 , GLY C:286 , ASP C:290 , ARG C:294 , LEU C:340 , ASP C:351
BINDING SITE FOR RESIDUE ZOP C 600
4
AC4
SOFTWARE
ILE D:211 , GLY D:212 , VAL D:219 , ALA D:230 , LYS D:232 , GLU D:245 , LEU D:260 , LEU D:278 , SER D:280 , ASP D:281 , TYR D:282 , HIS D:283 , GLU D:284 , HIS D:285 , GLY D:286 , ASP D:290 , LEU D:340 , ASP D:351
BINDING SITE FOR RESIDUE ZOP D 600
5
AC5
SOFTWARE
ILE E:211 , GLY E:212 , VAL E:219 , ALA E:230 , LYS E:232 , GLU E:245 , LEU E:260 , LEU E:278 , SER E:280 , ASP E:281 , TYR E:282 , HIS E:283 , GLU E:284 , HIS E:285 , GLY E:286 , ASP E:290 , ARG E:294 , LEU E:340
BINDING SITE FOR RESIDUE ZOP E 600
[
close Site info
]
SAPs(SNPs)/Variants
(13, 65)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_022344 (T200I, chain A/B/C/D/E, )
02: VAR_029481 (K232E, chain A/B/C/D/E, )
03: VAR_029482 (S241L, chain A/B/C/D/E, )
04: VAR_066720 (D266Y, chain A/B/C/D/E, )
05: VAR_029483 (N267H, chain A/B/C/D/E, )
06: VAR_041413 (Y291C, chain A/B/C/D/E, )
07: VAR_022345 (M318R, chain A/B/C/D/E, )
08: VAR_066721 (D351G, chain A/B/C/D/E, )
09: VAR_066722 (T375I, chain A/B/C/D/E, )
10: VAR_022346 (D400G, chain A/B/C/D/E, )
11: VAR_022347 (R487P, chain A/B/C/D/E, )
12: VAR_029484 (R487Q, chain A/B/C/D/E, )
13: VAR_029485 (R487W, chain A/B/C/D/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_022344
T
200
I
TGFR1_HUMAN
Disease (LDS1)
---
A/B/C/D/E
T
200
I
02
UniProt
VAR_029481
K
232
E
TGFR1_HUMAN
Disease (LDS1)
---
A/B/C/D/E
K
232
E
03
UniProt
VAR_029482
S
241
L
TGFR1_HUMAN
Disease (LDS1)
---
A/B/C/D/E
S
241
L
04
UniProt
VAR_066720
D
266
Y
TGFR1_HUMAN
Disease (LDS1)
---
A/B/C/D/E
D
266
Y
05
UniProt
VAR_029483
N
267
H
TGFR1_HUMAN
Unclassified
---
A/B/C/D/E
N
267
H
06
UniProt
VAR_041413
Y
291
C
TGFR1_HUMAN
Polymorphism
35974499
A/B/C/D/E
Y
291
C
07
UniProt
VAR_022345
M
318
R
TGFR1_HUMAN
Disease (LDS1)
---
A/B/C/D/E
M
318
R
08
UniProt
VAR_066721
D
351
G
TGFR1_HUMAN
Disease (LDS1)
---
A/B/C/D/E
D
351
G
09
UniProt
VAR_066722
T
375
I
TGFR1_HUMAN
Disease (LDS1)
---
A/B/C/D/E
T
375
I
10
UniProt
VAR_022346
D
400
G
TGFR1_HUMAN
Disease (LDS1)
---
A/B/C/D/E
D
400
G
11
UniProt
VAR_022347
R
487
P
TGFR1_HUMAN
Disease (LDS1)
---
A/B/C/D/E
R
487
P
12
UniProt
VAR_029484
R
487
Q
TGFR1_HUMAN
Disease (LDS1)
---
A/B/C/D/E
R
487
Q
13
UniProt
VAR_029485
R
487
W
TGFR1_HUMAN
Disease (LDS1)
---
A/B/C/D/E
R
487
W
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 15)
Info
All PROSITE Patterns/Profiles
1: GS (A:175-204,B:175-204,C:175-204,D:17...)
2: PROTEIN_KINASE_ATP (A:211-232,B:211-232,C:211-232,D:21...)
3: PROTEIN_KINASE_ST (A:329-341,B:329-341,C:329-341,D:32...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GS
PS51256
GS domain profile.
TGFR1_HUMAN
175-204
5
A:175-204
B:175-204
C:175-204
D:175-204
E:175-204
2
PROTEIN_KINASE_ATP
PS00107
Protein kinases ATP-binding region signature.
TGFR1_HUMAN
211-232
5
A:211-232
B:211-232
C:211-232
D:211-232
E:211-232
3
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
TGFR1_HUMAN
329-341
5
A:329-341
B:329-341
C:329-341
D:329-341
E:329-341
[
close PROSITE info
]
Exons
(7, 35)
Info
All Exons
Exon 1.3 (A:171-192 | B:171-192 | C:171-192 ...)
Exon 1.4 (A:192-269 | B:192-269 | C:192-269 ...)
Exon 1.5 (A:269-325 | B:269-325 | C:269-325 ...)
Exon 1.6 (A:325-377 | B:325-377 | C:325-377 ...)
Exon 1.7 (A:377-419 | B:377-419 | C:377-419 ...)
Exon 1.8 (A:419-462 | B:419-462 | C:419-462 ...)
Exon 1.9b (A:463-500 | B:463-500 | C:463-500 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2/1.3
2: Boundary 1.3/1.4
3: Boundary 1.4/1.5
4: Boundary 1.5/1.6
5: Boundary 1.6/1.7
6: Boundary 1.7/1.8
7: Boundary 1.8/1.9b
8: Boundary 1.9b/-
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
ENST00000374994
1
ENSE00001090681
chr9:
101867412-101867584
173
TGFR1_HUMAN
1-33
33
0
-
-
1.2
ENST00000374994
2
ENSE00001149190
chr9:
101891137-101891382
246
TGFR1_HUMAN
33-115
83
0
-
-
1.3
ENST00000374994
3
ENSE00001149139
chr9:
101894791-101895021
231
TGFR1_HUMAN
115-192
78
5
A:171-192
B:171-192
C:171-192
D:171-192
E:171-192
22
22
22
22
22
1.4
ENST00000374994
4
ENSE00001090680
chr9:
101900141-101900371
231
TGFR1_HUMAN
192-269
78
5
A:192-269
B:192-269
C:192-269
D:192-269
E:192-269
78
78
78
78
78
1.5
ENST00000374994
5
ENSE00001643263
chr9:
101904818-101904985
168
TGFR1_HUMAN
269-325
57
5
A:269-325
B:269-325
C:269-325
D:269-325
E:269-325
57
57
57
57
57
1.6
ENST00000374994
6
ENSE00000926563
chr9:
101907014-101907170
157
TGFR1_HUMAN
325-377
53
5
A:325-377
B:325-377
C:325-377
D:325-377
E:325-377
53
53
53
53
53
1.7
ENST00000374994
7
ENSE00000926564
chr9:
101908767-101908891
125
TGFR1_HUMAN
377-419
43
5
A:377-419
B:377-419
C:377-419
D:377-419
E:377-419
43
43
43
43
43
1.8
ENST00000374994
8
ENSE00000926565
chr9:
101909936-101910066
131
TGFR1_HUMAN
419-462
44
5
A:419-462
B:419-462
C:419-462
D:419-462
E:419-462
44
44
44
44
44
1.9b
ENST00000374994
9b
ENSE00001822848
chr9:
101911462-101916585
5124
TGFR1_HUMAN
463-503
41
5
A:463-500
B:463-500
C:463-500
D:463-500
E:463-500
38
38
38
38
38
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 10)
Info
all PFAM domains
1a: PFAM_Pkinase_2x7oE01 (E:205-492)
1b: PFAM_Pkinase_2x7oE02 (E:205-492)
1c: PFAM_Pkinase_2x7oE03 (E:205-492)
1d: PFAM_Pkinase_2x7oE04 (E:205-492)
1e: PFAM_Pkinase_2x7oE05 (E:205-492)
2a: PFAM_TGF_beta_GS_2x7oE06 (E:175-203)
2b: PFAM_TGF_beta_GS_2x7oE07 (E:175-203)
2c: PFAM_TGF_beta_GS_2x7oE08 (E:175-203)
2d: PFAM_TGF_beta_GS_2x7oE09 (E:175-203)
2e: PFAM_TGF_beta_GS_2x7oE10 (E:175-203)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PKinase
(934)
Family
:
Pkinase
(680)
Homo sapiens (Human)
(521)
1a
Pkinase-2x7oE01
E:205-492
1b
Pkinase-2x7oE02
E:205-492
1c
Pkinase-2x7oE03
E:205-492
1d
Pkinase-2x7oE04
E:205-492
1e
Pkinase-2x7oE05
E:205-492
Clan
:
no clan defined [family: TGF_beta_GS]
(12)
Family
:
TGF_beta_GS
(12)
Homo sapiens (Human)
(12)
2a
TGF_beta_GS-2x7oE06
E:175-203
2b
TGF_beta_GS-2x7oE07
E:175-203
2c
TGF_beta_GS-2x7oE08
E:175-203
2d
TGF_beta_GS-2x7oE09
E:175-203
2e
TGF_beta_GS-2x7oE10
E:175-203
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