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3LCD
Asym. Unit
Info
Asym.Unit (53 KB)
Biol.Unit 1 (48 KB)
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(1)
Title
:
INHIBITOR BOUND TO A DFG-IN STRUCTURE OF THE KINASE DOMAIN OF CSF-1R
Authors
:
S. Kamtekar, J. E. Day, B. A. Reitz, K. J. Mathis, M. J. Meyers
Date
:
10 Jan 10 (Deposition) - 02 Mar 10 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Kinase Cfms Csf-1R Csf Tyrosine-Kinase Colony Stimulating Factor 1 Receptor, Atp-Binding, Disulfide Bond, Glycoprotein, Immunoglobulin Domain, Kinase, Membrane, Nucleotide-Binding, Phosphoprotein, Proto- Oncogene, Receptor, Transferase, Transmembrane, Tyrosine-Protein Kinase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. J. Meyers, M. Pelc, S. Kamtekar, J. Day, G. I. Poda, M. K. Hall, M. L. Michener, B. A. Reitz, K. J. Mathis, B. S. Pierce, M. D. Parikh, D. A. Mischke, S. A. Long, J. J. Parlow, D. R. Anderson, A. Thorarensen
Structure-Based Drug Design Enables Conversion Of A Dfg-In Binding Csf-1R Kinase Inhibitor To A Dfg-Out Binding Mode
Bioorg. Med. Chem. Lett. V. 20 1543 2010
[
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Hetero Components
(2, 3)
Info
All Hetero Components
1a: N~3~-(2,6-DICHLOROBENZYL)-5-(4-{[(... (BDYa)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BDY
1
Ligand/Ion
N~3~-(2,6-DICHLOROBENZYL)-5-(4-{[(2R)-2-(PYRROLIDIN-1-YLMETHYL)PYRROLIDIN-1-YL]CARBONYL}PHENYL)PYRAZINE-2,3-DIAMINE
2
SO4
2
Ligand/Ion
SULFATE 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
TYR A:668 , ASN A:788 , GLY A:789
BINDING SITE FOR RESIDUE SO4 A 1
2
AC2
SOFTWARE
ARG A:777 , ARG A:801 , TYR A:809 , VAL A:811 , LYS A:812 , GLY A:813 , ALA A:815
BINDING SITE FOR RESIDUE SO4 A 2
3
AC3
SOFTWARE
HOH A:14 , HOH A:47 , HOH A:65 , LEU A:588 , VAL A:596 , ALA A:614 , GLU A:664 , TYR A:665 , CYS A:666 , TYR A:668 , GLY A:669 , ARG A:782 , LEU A:785 , ASP A:796
BINDING SITE FOR RESIDUE BDY A 923
[
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]
SAPs(SNPs)/Variants
(14, 14)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_067397 (G589E, chain A, )
02: VAR_067398 (E633K, chain A, )
03: VAR_072081 (C653R, chain A, )
04: VAR_067401 (M766T, chain A, )
05: VAR_067402 (A770P, chain A, )
06: VAR_067404 (I775N, chain A, )
07: VAR_067405 (I794T, chain A, )
08: VAR_067406 (D837Y, chain A, )
09: VAR_072082 (I843F, chain A, )
10: VAR_067407 (F849S, chain A, )
11: VAR_067409 (L868P, chain A, )
12: VAR_067410 (M875T, chain A, )
13: VAR_067411 (P878T, chain A, )
14: VAR_072083 (I906T, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_067397
G
589
E
CSF1R_HUMAN
Disease (HDLS)
---
A
G
589
E
02
UniProt
VAR_067398
E
633
K
CSF1R_HUMAN
Disease (HDLS)
---
A
E
633
K
03
UniProt
VAR_072081
C
653
R
CSF1R_HUMAN
Disease (HDLS)
---
A
C
653
R
04
UniProt
VAR_067401
M
766
T
CSF1R_HUMAN
Disease (HDLS)
---
A
M
766
T
05
UniProt
VAR_067402
A
770
P
CSF1R_HUMAN
Disease (HDLS)
---
A
A
770
P
06
UniProt
VAR_067404
I
775
N
CSF1R_HUMAN
Disease (HDLS)
---
A
I
775
N
07
UniProt
VAR_067405
I
794
T
CSF1R_HUMAN
Disease (HDLS)
---
A
I
794
T
08
UniProt
VAR_067406
D
837
Y
CSF1R_HUMAN
Disease (HDLS)
---
A
D
837
Y
09
UniProt
VAR_072082
I
843
F
CSF1R_HUMAN
Disease (HDLS)
---
A
I
843
F
10
UniProt
VAR_067407
F
849
S
CSF1R_HUMAN
Disease (HDLS)
---
A
F
849
S
11
UniProt
VAR_067409
L
868
P
CSF1R_HUMAN
Disease (HDLS)
---
A
L
868
P
12
UniProt
VAR_067410
M
875
T
CSF1R_HUMAN
Disease (HDLS)
---
A
M
875
T
13
UniProt
VAR_067411
P
878
T
CSF1R_HUMAN
Disease (HDLS)
---
A
P
878
T
14
UniProt
VAR_072083
I
906
T
CSF1R_HUMAN
Disease (HDLS)
---
A
I
906
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:588-616)
2: RECEPTOR_TYR_KIN_III (A:641-654)
3: PROTEIN_KINASE_TYR (A:774-786)
;
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.
CSF1R_HUMAN
588-616
1
A:588-616
2
RECEPTOR_TYR_KIN_III
PS00240
Receptor tyrosine kinase class III signature.
CSF1R_HUMAN
641-654
1
A:641-654
3
PROTEIN_KINASE_TYR
PS00109
Tyrosine protein kinases specific active-site signature.
CSF1R_HUMAN
774-786
1
A:774-786
[
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]
Exons
(10, 10)
Info
All Exons
Exon 1.13a (A:558-585)
Exon 1.13d (A:585-620)
Exon 1.14 (A:620-657)
Exon 1.15b (A:657-681)
Exon 1.17 (A:741-741)
Exon 1.18 (A:741-773 (gaps))
Exon 1.19 (A:774-814 (gaps))
Exon 1.20 (A:815-852)
Exon 1.21 (A:852-885)
Exon 1.22b (A:885-913)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.11/1.13a
02: Boundary 1.13a/1.13d
03: Boundary 1.13d/1.14
04: Boundary 1.14/1.15b
05: Boundary 1.15b/1.17
06: Boundary 1.17/1.18
07: Boundary 1.18/1.19
08: Boundary 1.19/1.20
09: Boundary 1.20/1.21
10: Boundary 1.21/1.22b
11: Boundary 1.22b/1.23c
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
ENST00000286301
1
ENSE00000841168
chr5:
149492935-149492824
112
CSF1R_HUMAN
-
0
0
-
-
1.2b
ENST00000286301
2b
ENSE00001366842
chr5:
149466170-149465942
229
CSF1R_HUMAN
1-17
17
0
-
-
1.3
ENST00000286301
3
ENSE00001023095
chr5:
149460587-149460330
258
CSF1R_HUMAN
17-103
87
0
-
-
1.4
ENST00000286301
4
ENSE00001023084
chr5:
149459899-149459615
285
CSF1R_HUMAN
103-198
96
0
-
-
1.5
ENST00000286301
5
ENSE00001023099
chr5:
149457811-149457675
137
CSF1R_HUMAN
198-243
46
0
-
-
1.6a
ENST00000286301
6a
ENSE00001023081
chr5:
149456998-149456839
160
CSF1R_HUMAN
244-297
54
0
-
-
1.7
ENST00000286301
7
ENSE00001023101
chr5:
149453056-149452864
193
CSF1R_HUMAN
297-361
65
0
-
-
1.8
ENST00000286301
8
ENSE00001023092
chr5:
149450134-149450019
116
CSF1R_HUMAN
361-400
40
0
-
-
1.9
ENST00000286301
9
ENSE00001023097
chr5:
149449865-149449745
121
CSF1R_HUMAN
400-440
41
0
-
-
1.10
ENST00000286301
10
ENSE00001023094
chr5:
149449626-149449436
191
CSF1R_HUMAN
440-504
65
0
-
-
1.11
ENST00000286301
11
ENSE00001023090
chr5:
149447893-149447778
116
CSF1R_HUMAN
504-542
39
0
-
-
1.13a
ENST00000286301
13a
ENSE00001023078
chr5:
149441412-149441286
127
CSF1R_HUMAN
543-585
43
1
A:558-585
28
1.13d
ENST00000286301
13d
ENSE00001023098
chr5:
149441158-149441054
105
CSF1R_HUMAN
585-620
36
1
A:585-620
36
1.14
ENST00000286301
14
ENSE00001023088
chr5:
149440535-149440425
111
CSF1R_HUMAN
620-657
38
1
A:620-657
38
1.15b
ENST00000286301
15b
ENSE00001023096
chr5:
149439425-149439263
163
CSF1R_HUMAN
657-711
55
1
A:657-681
25
1.17
ENST00000286301
17
ENSE00001023083
chr5:
149437155-149437067
89
CSF1R_HUMAN
711-741
31
1
A:741-741
1
1.18
ENST00000286301
18
ENSE00001023077
chr5:
149436947-149436850
98
CSF1R_HUMAN
741-773
33
1
A:741-773 (gaps)
33
1.19
ENST00000286301
19
ENSE00001023079
chr5:
149435904-149435782
123
CSF1R_HUMAN
774-814
41
1
A:774-814 (gaps)
41
1.20
ENST00000286301
20
ENSE00001684899
chr5:
149435700-149435589
112
CSF1R_HUMAN
815-852
38
1
A:815-852
38
1.21
ENST00000286301
21
ENSE00001023100
chr5:
149434899-149434800
100
CSF1R_HUMAN
852-885
34
1
A:852-885
34
1.22b
ENST00000286301
22b
ENSE00001023085
chr5:
149433993-149433885
109
CSF1R_HUMAN
885-921
37
1
A:885-913
29
1.23c
ENST00000286301
23c
ENSE00001083274
chr5:
149433787-149432854
934
CSF1R_HUMAN
922-972
51
0
-
-
[
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3lcda_ (A:)
View:
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Classes
(
)
(
)
Folds
(
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(
)
Superfamilies
(
)
(
)
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(
)
(
)
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
d3lcda_
A:
[
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_3lcdA01 (A:563-665)
2a: CATH_3lcdA02 (A:666-910)
View:
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(
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(
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(
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Topologies
(
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(
)
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
3lcdA01
A:563-665
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
3lcdA02
A:666-910
[
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Pkinase_Tyr_3lcdA01 (A:582-910)
View:
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Clans
(
)
(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PKinase
(934)
Family
:
Pkinase_Tyr
(229)
Homo sapiens (Human)
(202)
1a
Pkinase_Tyr-3lcdA01
A:582-910
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Asymmetric Unit 1
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