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3II5
Biol. Unit 1
Info
Asym.Unit (93 KB)
Biol.Unit 1 (46 KB)
Biol.Unit 2 (45 KB)
Biol.Unit 3 (87 KB)
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Title
:
THE COMPLEX OF WILD-TYPE B-RAF WITH PYRAZOLO PYRIMIDINE INHIBITOR
Authors
:
W. Xu, D. Breger, N. Torres, M. Dutia, D. Powell, G. Ciszewski
Date
:
31 Jul 09 (Deposition) - 10 Nov 09 (Release) - 17 Nov 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.79
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (1x)
Keywords
:
B-Raf, Kinase, Protein-Inhibitor Complex, Acetylation, Atp- Binding, Cardiomyopathy, Cytoplasm, Disease Mutation, Metal-Binding, Nucleotide-Binding, Phorbol-Ester Binding, Phosphoprotein, Polymorphism, Proto-Oncogene, Serine/Threonine-Protein Kinase, Transferase, Zinc, Zinc- Finger
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. M. Berger, N. Torres, M. Dutia, D. Powell, G. Ciszewski, A. Gopalsamy, J. I. Levin, K. H. Kim, W. Xu, J. Wilhelm, Y. Hu, K. Collins, L. Feldberg, S. Kim, E. Frommer, D. Wojciechowicz, R. Mallon
Non-Hinge-Binding Pyrazolo[1, 5-A]Pyrimidines As Potent B-Raf Kinase Inhibitors.
Bioorg. Med. Chem. Lett. V. 19 6519 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 3)
Info
All Hetero Components
1a: N-[3-(3-{4-[(DIMETHYLAMINO)METHYL]... (831a)
1b: N-[3-(3-{4-[(DIMETHYLAMINO)METHYL]... (831b)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
831
1
Ligand/Ion
N-[3-(3-{4-[(DIMETHYLAMINO)METHYL]PHENYL}PYRAZOLO[1,5-A]PYRIMIDIN-7-YL)PHENYL]-3-(TRIFLUOROMETHYL)BENZAMIDE
2
PO4
2
Ligand/Ion
PHOSPHATE ION
[
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]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:16 , ILE A:462 , LYS A:482 , GLU A:500 , LEU A:513 , THR A:528 , HIS A:573 , GLY A:592 , ASP A:593 , PHE A:594 , ARG B:670
BINDING SITE FOR RESIDUE 831 A 1
2
AC2
SOFTWARE
HOH A:6 , ASP A:447 , TRP A:449 , ARG A:505 , TRP B:449 , ARG B:505
BINDING SITE FOR RESIDUE PO4 A 726
3
AC3
SOFTWARE
GLN A:529 , THR A:588 , LYS A:590 , LYS B:590
BINDING SITE FOR RESIDUE PO4 A 2
[
close Site info
]
SAPs(SNPs)/Variants
(35, 35)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_018613 (R461I, chain A, )
02: VAR_018614 (I462S, chain A, )
03: VAR_018615 (G463E, chain A, )
04: VAR_018616 (G463V, chain A, )
05: VAR_018617 (G465A, chain A, )
06: VAR_018618 (G465E, chain A, )
07: VAR_018512 (G465V, chain A, )
08: VAR_035096 (S466A, chain A, )
09: VAR_035097 (F467S, chain A, )
10: VAR_018620 (G468A, chain A, )
11: VAR_018621 (G468E, chain A, )
12: VAR_018622 (G468R, chain A, )
13: VAR_040392 (G468V, chain A, )
14: VAR_026115 (L484F, chain A, )
15: VAR_026116 (K498E, chain A, )
16: VAR_058625 (K498N, chain A, )
17: VAR_026117 (E500G, chain A, )
18: VAR_026118 (E500K, chain A, )
19: VAR_058626 (L524P, chain A, )
20: VAR_058627 (W530C, chain A, )
21: VAR_065173 (N579D, chain A, )
22: VAR_026119 (N580D, chain A, )
23: VAR_040393 (N580S, chain A, )
24: VAR_018623 (E585K, chain A, )
25: VAR_018624 (D593G, chain A, )
26: VAR_018625 (F594L, chain A, )
27: VAR_018626 (G595R, chain A, )
28: VAR_035098 (G595V, chain A, )
29: VAR_018513 (L596R, chain A, )
30: VAR_018627 (L596V, chain A, )
31: VAR_058628 (T598R, chain A, )
32: VAR_018628 (V599D, chain A, )
33: VAR_018629 (V599E, chain A, )
34: VAR_058630 (D637E, chain A, )
35: VAR_058631 (Q708R, chain A, )
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
R
461
I
02
UniProt
VAR_018614
I
463
S
BRAF_HUMAN
Disease (CRC)
---
A
I
462
S
03
UniProt
VAR_018615
G
464
E
BRAF_HUMAN
Disease (CRC)
---
A
G
463
E
04
UniProt
VAR_018616
G
464
V
BRAF_HUMAN
Unclassified
---
A
G
463
V
05
UniProt
VAR_018617
G
466
A
BRAF_HUMAN
Unclassified
---
A
G
465
A
06
UniProt
VAR_018618
G
466
E
BRAF_HUMAN
Unclassified
---
A
G
465
E
07
UniProt
VAR_018512
G
466
V
BRAF_HUMAN
Disease (LNCR)
---
A
G
465
V
08
UniProt
VAR_035096
S
467
A
BRAF_HUMAN
Disease (CFC1)
---
A
S
466
A
09
UniProt
VAR_035097
F
468
S
BRAF_HUMAN
Disease (CFC1)
---
A
F
467
S
10
UniProt
VAR_018620
G
469
A
BRAF_HUMAN
Disease (NHL)
---
A
G
468
A
11
UniProt
VAR_018621
G
469
E
BRAF_HUMAN
Disease (CFC1)
---
A
G
468
E
12
UniProt
VAR_018622
G
469
R
BRAF_HUMAN
Disease (NHL)
---
A
G
468
R
13
UniProt
VAR_040392
G
469
V
BRAF_HUMAN
Unclassified
---
A
G
468
V
14
UniProt
VAR_026115
L
485
F
BRAF_HUMAN
Disease (CFC1)
---
A
L
484
F
15
UniProt
VAR_026116
K
499
E
BRAF_HUMAN
Disease (CFC1)
---
A
K
498
E
16
UniProt
VAR_058625
K
499
N
BRAF_HUMAN
Disease (CFC1)
---
A
K
498
N
17
UniProt
VAR_026117
E
501
G
BRAF_HUMAN
Disease (CFC1)
---
A
E
500
G
18
UniProt
VAR_026118
E
501
K
BRAF_HUMAN
Disease (CFC1)
---
A
E
500
K
19
UniProt
VAR_058626
L
525
P
BRAF_HUMAN
Disease (CFC1)
---
A
L
524
P
20
UniProt
VAR_058627
W
531
C
BRAF_HUMAN
Disease (NS7)
---
A
W
530
C
21
UniProt
VAR_065173
N
580
D
BRAF_HUMAN
Disease (CFC1)
---
A
N
579
D
22
UniProt
VAR_026119
N
581
D
BRAF_HUMAN
Disease (CFC1)
---
A
N
580
D
23
UniProt
VAR_040393
N
581
S
BRAF_HUMAN
Unclassified
---
A
N
580
S
24
UniProt
VAR_018623
E
586
K
BRAF_HUMAN
Unclassified
---
A
E
585
K
25
UniProt
VAR_018624
D
594
G
BRAF_HUMAN
Disease (NHL)
---
A
D
593
G
26
UniProt
VAR_018625
F
595
L
BRAF_HUMAN
Unclassified
---
A
F
594
L
27
UniProt
VAR_018626
G
596
R
BRAF_HUMAN
Unclassified
---
A
G
595
R
28
UniProt
VAR_035098
G
596
V
BRAF_HUMAN
Disease (CFC1)
---
A
G
595
V
29
UniProt
VAR_018513
L
597
R
BRAF_HUMAN
Disease (LNCR)
---
A
L
596
R
30
UniProt
VAR_018627
L
597
V
BRAF_HUMAN
Disease (NS7)
---
A
L
596
V
31
UniProt
VAR_058628
T
599
R
BRAF_HUMAN
Disease (CFC1)
---
A
T
598
R
32
UniProt
VAR_018628
V
600
D
BRAF_HUMAN
Unclassified
---
A
V
599
D
33
UniProt
VAR_018629
V
600
E
BRAF_HUMAN
Disease (CRC)
---
A
V
599
E
34
UniProt
VAR_058630
D
638
E
BRAF_HUMAN
Disease (CFC1)
---
A
D
637
E
35
UniProt
VAR_058631
Q
709
R
BRAF_HUMAN
Disease (CFC1)
---
A
Q
708
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:462-482)
2: PROTEIN_KINASE_ST (A:571-583)
;
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
1
A:462-482
-
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
BRAF_HUMAN
572-584
1
A:571-583
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3ii5a_ (A:)
1b: SCOP_d3ii5b_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
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
:
automated matches
(542)
Human (Homo sapiens) [TaxId: 9606]
(452)
1a
d3ii5a_
A:
1b
d3ii5b_
B:
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3ii5A01 (A:447-532)
1b: CATH_3ii5B01 (B:448-532)
2a: CATH_3ii5A02 (A:533-719)
2b: CATH_3ii5B02 (B:533-720)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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
3ii5A01
A:447-532
1b
3ii5B01
B:448-532
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
3ii5A02
A:533-719
2b
3ii5B02
B:533-720
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Chain A
Asymmetric Unit 1
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Asym.Unit (93 KB)
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