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.
3SKC
Asym. Unit
Info
Asym.Unit (95 KB)
Biol.Unit 1 (44 KB)
Biol.Unit 2 (48 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN B-RAF KINASE IN COMPLEX WITH AN AMIDE LINKED PYRAZOLOPYRIDINE INHIBITOR
Authors
:
W. C. Voegtli, H. L. Sturgis
Date
:
22 Jun 11 (Deposition) - 17 Aug 11 (Release) - 14 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Kinase, Atp-Competitive Inhibitor, Transferase, Ras, Mek, C-Raf, Transferase-Transferase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Wenglowsky, K. A. Ahrendt, A. J. Buckmelter, B. Feng, S. L. Gloor, S. Gradl, J. Grina, J. D. Hansen, E. R. Laird, P. Lunghofer, S. Mathieu, D. Moreno, B. Newhouse, L. Ren, T. Risom, J. Rudolph, J. Seo, H. L. Sturgis, W. C. Voegtli, Z. Wen
Pyrazolopyridine Inhibitors Of B-Rafv600E. Part 2: Structure-Activity Relationships.
Bioorg. Med. Chem. Lett. V. 21 5533 2011
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: 2,6-DIFLUORO-N-[(5S)-3-METHOXY-5H-... (BR2a)
1b: 2,6-DIFLUORO-N-[(5S)-3-METHOXY-5H-... (BR2b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BR2
2
Ligand/Ion
2,6-DIFLUORO-N-[(5S)-3-METHOXY-5H-PYRAZOLO[3,4-B]PYRIDIN-5-YL]-3-[(PHENYLSULFONYL)AMINO]BENZAMIDE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:481 , LYS A:483 , LEU A:505 , LEU A:514 , PHE A:516 , ILE A:527 , THR A:529 , GLN A:530 , TRP A:531 , CYS A:532 , ASP A:594 , PHE A:595
BINDING SITE FOR RESIDUE BR2 A 801
2
AC2
SOFTWARE
ALA B:481 , LYS B:483 , LEU B:505 , LEU B:514 , THR B:529 , GLN B:530 , TRP B:531 , CYS B:532 , PHE B:583 , ASP B:594 , PHE B:595 , GLY B:596
BINDING SITE FOR RESIDUE BR2 B 801
[
close Site info
]
SAPs(SNPs)/Variants
(37, 67)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_018613 (R462I, chain A/B, )
02: VAR_018614 (I463S, chain A/B, )
03: VAR_018615 (G464E, chain A/B, )
04: VAR_018616 (G464V, chain A/B, )
05: VAR_018617 (G466A, chain A/B, )
06: VAR_018618 (G466E, chain A/B, )
07: VAR_018512 (G466V, chain A/B, )
08: VAR_035096 (S467A, chain A/B, )
09: VAR_035097 (F468S, chain A/B, )
10: VAR_018620 (G469A, chain A/B, )
11: VAR_018621 (G469E, chain A/B, )
12: VAR_018622 (G469R, chain A/B, )
13: VAR_040392 (G469V, chain A/B, )
14: VAR_026115 (L485F, chain A/B, )
15: VAR_026116 (K499E, chain A/B, )
16: VAR_058625 (K499N, chain A/B, )
17: VAR_026117 (E501G, chain A/B, )
18: VAR_026118 (E501K, chain A/B, )
19: VAR_058626 (L525P, chain A/B, )
20: VAR_058627 (W531C, chain A/B, )
21: VAR_065173 (N580D, chain A/B, )
22: VAR_026119 (N581D, chain A/B, )
23: VAR_040393 (N581S, chain A/B, )
24: VAR_018623 (E586K, chain A/B, )
25: VAR_018624 (D594G, chain A/B, )
26: VAR_018625 (F595L, chain A/B, )
27: VAR_018626 (G596R, chain A/B, )
28: VAR_035098 (G596V, chain A/B, )
29: VAR_018513 (L597R, chain B, )
30: VAR_018627 (L597V, chain B, )
31: VAR_058628 (T599R, chain B, )
32: VAR_018628 (V600D, chain B, )
33: VAR_018629 (V600E, chain B, )
34: VAR_018630 (K601E, chain B, )
35: VAR_058629 (K601Q, chain B, )
36: VAR_058630 (D638E, chain A/B, )
37: VAR_058631 (Q709R, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_018613
R
462
I
BRAF_HUMAN
Disease (CRC)
---
A/B
R
462
I
02
UniProt
VAR_018614
I
463
S
BRAF_HUMAN
Disease (CRC)
---
A/B
I
463
S
03
UniProt
VAR_018615
G
464
E
BRAF_HUMAN
Disease (CRC)
---
A/B
G
464
E
04
UniProt
VAR_018616
G
464
V
BRAF_HUMAN
Unclassified
---
A/B
G
464
V
05
UniProt
VAR_018617
G
466
A
BRAF_HUMAN
Unclassified
---
A/B
G
466
A
06
UniProt
VAR_018618
G
466
E
BRAF_HUMAN
Unclassified
---
A/B
G
466
E
07
UniProt
VAR_018512
G
466
V
BRAF_HUMAN
Disease (LNCR)
---
A/B
G
466
V
08
UniProt
VAR_035096
S
467
A
BRAF_HUMAN
Disease (CFC1)
---
A/B
S
467
A
09
UniProt
VAR_035097
F
468
S
BRAF_HUMAN
Disease (CFC1)
---
A/B
F
468
S
10
UniProt
VAR_018620
G
469
A
BRAF_HUMAN
Disease (NHL)
---
A/B
G
469
A
11
UniProt
VAR_018621
G
469
E
BRAF_HUMAN
Disease (CFC1)
---
A/B
G
469
E
12
UniProt
VAR_018622
G
469
R
BRAF_HUMAN
Disease (NHL)
---
A/B
G
469
R
13
UniProt
VAR_040392
G
469
V
BRAF_HUMAN
Unclassified
---
A/B
G
469
V
14
UniProt
VAR_026115
L
485
F
BRAF_HUMAN
Disease (CFC1)
---
A/B
L
485
F
15
UniProt
VAR_026116
K
499
E
BRAF_HUMAN
Disease (CFC1)
---
A/B
K
499
E
16
UniProt
VAR_058625
K
499
N
BRAF_HUMAN
Disease (CFC1)
---
A/B
K
499
N
17
UniProt
VAR_026117
E
501
G
BRAF_HUMAN
Disease (CFC1)
---
A/B
E
501
G
18
UniProt
VAR_026118
E
501
K
BRAF_HUMAN
Disease (CFC1)
---
A/B
E
501
K
19
UniProt
VAR_058626
L
525
P
BRAF_HUMAN
Disease (CFC1)
---
A/B
L
525
P
20
UniProt
VAR_058627
W
531
C
BRAF_HUMAN
Disease (NS7)
---
A/B
W
531
C
21
UniProt
VAR_065173
N
580
D
BRAF_HUMAN
Disease (CFC1)
---
A/B
N
580
D
22
UniProt
VAR_026119
N
581
D
BRAF_HUMAN
Disease (CFC1)
---
A/B
N
581
D
23
UniProt
VAR_040393
N
581
S
BRAF_HUMAN
Unclassified
---
A/B
N
581
S
24
UniProt
VAR_018623
E
586
K
BRAF_HUMAN
Unclassified
---
A/B
E
586
K
25
UniProt
VAR_018624
D
594
G
BRAF_HUMAN
Disease (NHL)
---
A/B
D
594
G
26
UniProt
VAR_018625
F
595
L
BRAF_HUMAN
Unclassified
---
A/B
F
595
L
27
UniProt
VAR_018626
G
596
R
BRAF_HUMAN
Unclassified
---
A/B
G
596
R
28
UniProt
VAR_035098
G
596
V
BRAF_HUMAN
Disease (CFC1)
---
A/B
G
596
V
29
UniProt
VAR_018513
L
597
R
BRAF_HUMAN
Disease (LNCR)
---
B
L
597
R
30
UniProt
VAR_018627
L
597
V
BRAF_HUMAN
Disease (NS7)
---
B
L
597
V
31
UniProt
VAR_058628
T
599
R
BRAF_HUMAN
Disease (CFC1)
---
B
T
599
R
32
UniProt
VAR_018628
V
600
D
BRAF_HUMAN
Unclassified
---
B
V
600
D
33
UniProt
VAR_018629
V
600
E
BRAF_HUMAN
Disease (CRC)
---
B
V
600
E
34
UniProt
VAR_018630
K
601
E
BRAF_HUMAN
Disease (CRC)
---
B
K
601
E
35
UniProt
VAR_058629
K
601
Q
BRAF_HUMAN
Disease (CFC1)
---
B
K
601
Q
36
UniProt
VAR_058630
D
638
E
BRAF_HUMAN
Disease (CFC1)
---
A/B
D
638
E
37
UniProt
VAR_058631
Q
709
R
BRAF_HUMAN
Disease (CFC1)
---
A/B
Q
709
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:463-483,B:463-483)
2: PROTEIN_KINASE_ST (A:572-584,B:572-584)
;
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.
BRAF_HUMAN
463-483
2
A:463-483
B:463-483
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
BRAF_HUMAN
572-584
2
A:572-584
B:572-584
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.12 (A:448-478 | B:448-478)
Exon 1.13 (A:478-506 | B:478-506)
Exon 1.14 (A:506-565 | B:506-565)
Exon 1.15a (A:565-581 | B:565-581)
Exon 1.16 (A:581-620 (gaps) | B:581-620)
Exon 1.17 (A:621-664 | B:621-664)
Exon 1.19 (A:665-709 | B:665-709)
Exon 1.20d (A:710-723 | B:710-723)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.11/1.12
2: Boundary 1.12/1.13
3: Boundary 1.13/1.14
4: Boundary 1.14/1.15a
5: Boundary 1.15a/1.16
6: Boundary 1.16/1.17
7: Boundary 1.17/1.19
8: Boundary 1.19/1.20d
9: Boundary 1.20d/-
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
1.1a
ENST00000288602
1a
ENSE00001154485
chr7:
140624564-140624366
199
BRAF_HUMAN
1-46
46
0
-
-
1.2
ENST00000288602
2
ENSE00001035281
chr7:
140550012-140549911
102
BRAF_HUMAN
47-80
34
0
-
-
1.3a
ENST00000288602
3a
ENSE00001035295
chr7:
140534672-140534409
264
BRAF_HUMAN
81-168
88
0
-
-
1.4
ENST00000288602
4
ENSE00001034889
chr7:
140508795-140508692
104
BRAF_HUMAN
169-203
35
0
-
-
1.6
ENST00000288602
6
ENSE00001034814
chr7:
140507862-140507760
103
BRAF_HUMAN
203-237
35
0
-
-
1.7
ENST00000288602
7
ENSE00001034880
chr7:
140501360-140501212
149
BRAF_HUMAN
238-287
50
0
-
-
1.8
ENST00000288602
8
ENSE00001034818
chr7:
140500281-140500162
120
BRAF_HUMAN
287-327
41
0
-
-
1.9
ENST00000288602
9
ENSE00001034830
chr7:
140494267-140494108
160
BRAF_HUMAN
327-380
54
0
-
-
1.10
ENST00000288602
10
ENSE00001034865
chr7:
140487384-140487348
37
BRAF_HUMAN
381-393
13
0
-
-
1.11
ENST00000288602
11
ENSE00001034844
chr7:
140482957-140482821
137
BRAF_HUMAN
393-438
46
0
-
-
1.12
ENST00000288602
12
ENSE00001034859
chr7:
140481493-140481376
118
BRAF_HUMAN
439-478
40
2
A:448-478
B:448-478
31
31
1.13
ENST00000288602
13
ENSE00001034883
chr7:
140477875-140477791
85
BRAF_HUMAN
478-506
29
2
A:478-506
B:478-506
29
29
1.14
ENST00000288602
14
ENSE00001034826
chr7:
140476888-140476712
177
BRAF_HUMAN
506-565
60
2
A:506-565
B:506-565
60
60
1.15a
ENST00000288602
15a
ENSE00001034811
chr7:
140454033-140453987
47
BRAF_HUMAN
565-581
17
2
A:565-581
B:565-581
17
17
1.16
ENST00000288602
16
ENSE00001034798
chr7:
140453193-140453075
119
BRAF_HUMAN
581-620
40
2
A:581-620 (gaps)
B:581-620
40
40
1.17
ENST00000288602
17
ENSE00001034817
chr7:
140449218-140449087
132
BRAF_HUMAN
621-664
44
2
A:621-664
B:621-664
44
44
1.19
ENST00000288602
19
ENSE00001034824
chr7:
140439746-140439612
135
BRAF_HUMAN
665-709
45
2
A:665-709
B:665-709
45
45
1.20d
ENST00000288602
20d
ENSE00001034876
chr7:
140434570-140434279
292
BRAF_HUMAN
710-766
57
2
A:710-723
B:710-723
14
14
[
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
(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
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 (95 KB)
Header - Asym.Unit
Biol.Unit 1 (44 KB)
Header - Biol.Unit 1
Biol.Unit 2 (48 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
3SKC
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
