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3LKJ
Asym. Unit
Info
Asym.Unit (72 KB)
Biol.Unit 1 (66 KB)
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(1)
Title
:
SMALL MOLECULE INHIBITION OF THE TNF FAMILY CYOKINE CD40 LIGAND THROUGH A SUBUNIT FRACTURE MECHANISM
Authors
:
L. F. Silvian, A. Whitty
Date
:
27 Jan 10 (Deposition) - 02 Feb 11 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Cd40L, Cd154, Tnf-Family Cytokine, Protein-Protein Interaction, Cell Membrane, Cytokine, Disease Mutation, Disulfide Bond, Glycoprotein, Membrane, Phosphoprotein, Secreted, Signal-Anchor, Transmembrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. F. Silvian, J. E. Friedman, K. Strauch, T. G. Cachero, E. S. Day, F. Qian, B. Cunningham, A. Fung, L. Sun, L. Su, Z. Zheng, G. Kumaravel, A. Whitty
Small Molecule Inhibition Of The Tnf Family Cytokine Cd40 Ligand Through A Subunit Fracture Mechanism.
Acs Chem. Biol. V. 6 636 2011
[
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Hetero Components
(2, 7)
Info
All Hetero Components
1a: (2R)-{[(2'-[(BIPHENYL-3-YLMETHYL)C... (LKJa)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
LKJ
1
Ligand/Ion
(2R)-{[(2'-[(BIPHENYL-3-YLMETHYL)CARBAMOYL]-6'-{[(2R)-2-(PYRROLIDIN-1-YLMETHYL)PYRROLIDIN-1-YL]CARBONYL}-6-{[(2R)-2-(1H-PYRROL-1-YLMETHYL)PYRROLIDIN-1-YL]CARBONYL}-4,4'-BIPYRIDIN-2-YL)CARBONYL]AMINO}(CYCLOHEXYL)ETHANOIC ACID
2
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
NAG A:3 , HOH A:48 , SER A:136 , CYS A:194 , GLU A:202 , ASN A:240 , VAL A:241
BINDING SITE FOR RESIDUE NAG A 2
2
AC2
SOFTWARE
NAG A:2
BINDING SITE FOR RESIDUE NAG A 3
3
AC3
SOFTWARE
NAG B:3 , ILE B:190 , SER B:192 , GLU B:202 , ARG B:207 , ASN B:240 , VAL B:241 , THR B:242
BINDING SITE FOR RESIDUE NAG B 2
4
AC4
SOFTWARE
NAG B:2 , GLU B:202
BINDING SITE FOR RESIDUE NAG B 3
5
AC5
SOFTWARE
LEU A:168 , TYR A:170 , VAL A:228 , GLU A:230 , LEU A:259 , LEU A:261 , ALA B:173 , HIS B:224 , LEU B:225 , HOH C:56 , HOH C:64 , HOH C:79 , GLN C:121 , ALA C:123 , HIS C:125 , TYR C:145 , TYR C:146 , TYR C:170 , TYR C:172 , ARG C:200 , HIS C:224 , LEU C:225 , LEU C:259 , LEU C:261
BINDING SITE FOR RESIDUE LKJ C 1
6
AC6
SOFTWARE
NAG C:3 , HOH C:7 , ILE C:190 , CYS C:194 , GLU C:202 , ASN C:240
BINDING SITE FOR RESIDUE NAG C 2
7
AC7
SOFTWARE
NAG C:2 , HOH C:54 , HOH C:68 , GLU C:202 , ILE C:204
BINDING SITE FOR RESIDUE NAG C 3
[
close Site info
]
SAPs(SNPs)/Variants
(29, 87)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_007514 (A123E, chain A/B/C, )
02: VAR_017926 (H125R, chain A/B/C, )
03: VAR_007515 (V126A, chain A/B/C, )
04: VAR_017931 (V126D, chain A/B/C, )
05: VAR_007517 (W140C, chain A/B/C, )
06: VAR_007518 (W140G, chain A/B/C, )
07: VAR_007519 (W140R, chain A/B/C, )
08: VAR_017932 (K143T, chain A/B/C, )
09: VAR_007520 (G144E, chain A/B/C, )
10: VAR_017922 (T147N, chain A/B/C, )
11: VAR_007521 (L155P, chain A/B/C, )
12: VAR_017923 (Y170C, chain A/B/C, )
13: VAR_017933 (A173D, chain A/B/C, )
14: VAR_017927 (Q174R, chain A/B/C, )
15: VAR_017934 (T176I, chain A/B/C, )
16: VAR_017935 (L195P, chain A/B/C, )
17: VAR_017936 (A208D, chain A/B/C, )
18: VAR_007522 (T211N, chain A/B/C, )
19: VAR_007523 (G219R, chain A/B/C, )
20: VAR_017937 (H224Y, chain A/B/C, )
21: VAR_017938 (G226A, chain A/B/C, )
22: VAR_007524 (G227V, chain A/B/C, )
23: VAR_007526 (L231S, chain A/B/C, )
24: VAR_007527 (A235P, chain A/B/C, )
25: VAR_017939 (V237E, chain A/B/C, )
26: VAR_007528 (T254M, chain A/B/C, )
27: VAR_017940 (G257D, chain A/B/C, )
28: VAR_017928 (G257S, chain A/B/C, )
29: VAR_017924 (L258S, chain A/B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_007514
A
123
E
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
A
123
E
02
UniProt
VAR_017926
H
125
R
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
H
125
R
03
UniProt
VAR_007515
V
126
A
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
V
126
A
04
UniProt
VAR_017931
V
126
D
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
V
126
D
05
UniProt
VAR_007517
W
140
C
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
W
140
C
06
UniProt
VAR_007518
W
140
G
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
W
140
G
07
UniProt
VAR_007519
W
140
R
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
W
140
R
08
UniProt
VAR_017932
K
143
T
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
K
143
T
09
UniProt
VAR_007520
G
144
E
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
G
144
E
10
UniProt
VAR_017922
T
147
N
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
T
147
N
11
UniProt
VAR_007521
L
155
P
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
L
155
P
12
UniProt
VAR_017923
Y
170
C
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
Y
170
C
13
UniProt
VAR_017933
A
173
D
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
A
173
D
14
UniProt
VAR_017927
Q
174
R
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
Q
174
R
15
UniProt
VAR_017934
T
176
I
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
T
176
I
16
UniProt
VAR_017935
L
195
P
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
L
195
P
17
UniProt
VAR_017936
A
208
D
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
A
208
D
18
UniProt
VAR_007522
T
211
N
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
T
211
N
19
UniProt
VAR_007523
G
219
R
CD40L_HUMAN
Polymorphism
148594123
A/B/C
G
219
R
20
UniProt
VAR_017937
H
224
Y
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
H
224
Y
21
UniProt
VAR_017938
G
226
A
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
G
226
A
22
UniProt
VAR_007524
G
227
V
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
G
227
V
23
UniProt
VAR_007526
L
231
S
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
L
231
S
24
UniProt
VAR_007527
A
235
P
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
A
235
P
25
UniProt
VAR_017939
V
237
E
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
V
237
E
26
UniProt
VAR_007528
T
254
M
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
T
254
M
27
UniProt
VAR_017940
G
257
D
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
G
257
D
28
UniProt
VAR_017928
G
257
S
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
G
257
S
29
UniProt
VAR_017924
L
258
S
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
L
258
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: TNF_2 (A:123-261,B:123-261,C:123-261)
2: TNF_1 (A:161-177,B:161-177,C:161-177)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TNF_2
PS50049
TNF family profile.
CD40L_HUMAN
123-261
3
A:123-261
B:123-261
C:123-261
2
TNF_1
PS00251
TNF family signature.
CD40L_HUMAN
161-177
3
A:161-177
B:161-177
C:161-177
[
close PROSITE info
]
Exons
(2, 6)
Info
All Exons
Exon 1.4 (A:121-137 | B:121-137 (gaps) | C:1...)
Exon 1.5 (A:137-261 (gaps) | B:137-261 (gaps...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3/1.4
2: Boundary 1.4/1.5
3: Boundary 1.5/-
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
ENST00000370629
1a
ENSE00001453187
X:135730352-135730563
212
CD40L_HUMAN
1-52
52
0
-
-
1.2
ENST00000370629
2
ENSE00000677016
X:135732425-135732556
132
CD40L_HUMAN
53-96
44
0
-
-
1.3
ENST00000370629
3
ENSE00000677017
X:135736532-135736589
58
CD40L_HUMAN
97-116
20
0
-
-
1.4
ENST00000370629
4
ENSE00000677018
X:135738515-135738577
63
CD40L_HUMAN
116-137
22
3
A:121-137
B:121-137 (gaps)
C:121-137
17
17
17
1.5
ENST00000370629
5
ENSE00001125156
X:135741198-135742549
1352
CD40L_HUMAN
137-261
125
3
A:137-261 (gaps)
B:137-261 (gaps)
C:137-261 (gaps)
125
125
125
[
close EXON info
]
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d3lkja_ (A:)
1b: SCOP_d3lkjb_ (B:)
1c: SCOP_d3lkjc_ (C:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
TNF-like
(100)
Superfamily
:
TNF-like
(100)
Family
:
TNF-like
(82)
Protein domain
:
automated matches
(12)
Human (Homo sapiens) [TaxId: 9606]
(8)
1a
d3lkja_
A:
1b
d3lkjb_
B:
1c
d3lkjc_
C:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_TNF_3lkjC01 (C:138-261)
1b: PFAM_TNF_3lkjC02 (C:138-261)
1c: PFAM_TNF_3lkjC03 (C:138-261)
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
C1q_TNF
(45)
Family
:
TNF
(37)
Homo sapiens (Human)
(26)
1a
TNF-3lkjC01
C:138-261
1b
TNF-3lkjC02
C:138-261
1c
TNF-3lkjC03
C:138-261
[
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]
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(currently selected atoms:
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Nucleic
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Protein & NOT PROSITE
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Chain C
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