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4C52
Asym. Unit
Info
Asym.Unit (115 KB)
Biol.Unit 1 (110 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BCL-XL IN COMPLEX WITH BENZOYLUREA COMPOUND (39B)
Authors
:
M. J. Roy, R. M. Brady, G. Lessene, P. M. Colman, P. E. Czabotar
Date
:
10 Sep 13 (Deposition) - 05 Feb 14 (Release) - 29 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Apoptosis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. M. Brady, A. Vom, M. J. Roy, N. Toovey, B. J. Smith, R. M. Moss, E. Hazis D. C. S. Huang, J. P. Parisot, H. Yang, I. P. Street, P. M. Colman, P. E. Czabotar, J. B. Baell, G. Lessene
De-Novo Designed Library Of Benzoylureas As Inhibitors Of Bcl-Xl: Synthesis, Structural And Biochemical Characterization.
J. Med. Chem. V. 57 1323 2014
[
close entry info
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Hetero Components
(3, 21)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
3a: (R)-2-(3-(3-((2,4-DIFLUOROPENYL)ET... (X0Da)
3b: (R)-2-(3-(3-((2,4-DIFLUOROPENYL)ET... (X0Db)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
12
Ligand/Ion
1,2-ETHANEDIOL
2
SO4
7
Ligand/Ion
SULFATE ION
3
X0D
2
Ligand/Ion
(R)-2-(3-(3-((2,4-DIFLUOROPENYL)ETHYNYL)BENZOYL)-3-PROPYLUREIDO)-3-(ISOBUTYLTHIO)PROPANOIC ACID
[
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]
Sites
(21, 21)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:101 , ALA A:104 , LEU A:112 , PHE A:123 , VAL A:126 , VAL A:127 , LEU A:130 , PHE A:143 , PHE A:146 , GLY A:147 , LEU A:150
BINDING SITE FOR RESIDUE X0D A 300
02
AC2
SOFTWARE
ARG A:102 , TYR B:101 , ARG B:103 , ALA B:104 , LEU B:112 , PHE B:123 , VAL B:126 , LEU B:130 , PHE B:143 , PHE B:146 , GLY B:147 , MET B:170 , HOH B:2048
BINDING SITE FOR RESIDUE X0D B 300
03
AC3
SOFTWARE
ASN B:136 , ARG B:139 , HOH B:2044
BINDING SITE FOR RESIDUE SO4 B1199
04
AC4
SOFTWARE
ARG A:6 , VAL A:10 , TRP A:24 , SER B:-1 , MET B:1 , SER B:2
BINDING SITE FOR RESIDUE SO4 A1197
05
AC5
SOFTWARE
ALA B:119 , TYR B:120 , ARG B:165 , TRP B:169
BINDING SITE FOR RESIDUE SO4 B1200
06
AC6
SOFTWARE
SER A:-1 , GLY A:-2 , GLU A:7 , TRP B:24 , SER B:25
BINDING SITE FOR RESIDUE SO4 A1198
07
AC7
SOFTWARE
LYS A:157 , ARG B:132
BINDING SITE FOR RESIDUE SO4 A1199
08
AC8
SOFTWARE
ASN A:136 , ARG A:139
BINDING SITE FOR RESIDUE SO4 A1200
09
AC9
SOFTWARE
GLU A:124 , GLN A:125 , ASN A:128 , HIS A:177 , ASN B:175 , ASP B:176 , HOH B:2066
BINDING SITE FOR RESIDUE SO4 A1201
10
BC1
SOFTWARE
ASN B:136 , TRP B:137 , GLY B:138
BINDING SITE FOR RESIDUE EDO B1201
11
BC2
SOFTWARE
ASN A:136 , TRP A:137 , GLY A:138 , TYR A:195
BINDING SITE FOR RESIDUE EDO A1202
12
BC3
SOFTWARE
THR A:115 , PRO A:116 , HOH A:2037 , PHE B:131 , TYR B:173 , HIS B:177 , HOH B:2039
BINDING SITE FOR RESIDUE EDO A1203
13
BC4
SOFTWARE
GLY A:-5 , GLN A:3 , HOH A:2067 , GLU B:179
BINDING SITE FOR RESIDUE EDO A1204
14
BC5
SOFTWARE
ASN A:128 , VAL A:135 , TYR A:173 , HIS A:177 , HOH B:2066
BINDING SITE FOR RESIDUE EDO B1207
15
BC6
SOFTWARE
LEU A:-3 , SER B:25 , GLN B:26
BINDING SITE FOR RESIDUE EDO B1202
16
BC7
SOFTWARE
SER A:110 , GLN B:121 , GLU B:124 , GLN B:125 , HOH B:2040
BINDING SITE FOR RESIDUE EDO B1203
17
BC8
SOFTWARE
GLU B:98 , ARG B:102
BINDING SITE FOR RESIDUE EDO B1204
18
BC9
SOFTWARE
SER A:14 , ALA A:84 , LYS A:87 , GLU B:7
BINDING SITE FOR RESIDUE EDO A1205
19
CC1
SOFTWARE
GLN A:88 , ARG A:91 , TYR B:15 , ARG B:91
BINDING SITE FOR RESIDUE EDO A1206
20
CC2
SOFTWARE
ASP A:11 , ARG A:91 , ARG B:91
BINDING SITE FOR RESIDUE EDO B1205
21
CC3
SOFTWARE
TYR B:15 , SER B:18 , THR B:115
BINDING SITE FOR RESIDUE EDO B1206
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(6, 12)
Info
All PROSITE Patterns/Profiles
1: BH4_1 (A:4-24,B:4-24)
2: BH4_2 (A:5-24,B:5-24)
3: BH3 (A:86-100,B:86-100)
4: BCL2_FAMILY (A:90-190,B:90-190)
5: BH1 (A:130-148,B:130-148)
6: BH2 (A:181-192,B:181-192)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BH4_1
PS01260
Apoptosis regulator, Bcl-2 family BH4 motif signature.
B2CL1_HUMAN
4-24
2
A:4-24
B:4-24
2
BH4_2
PS50063
Apoptosis regulator, Bcl-2 family BH4 motif profile.
B2CL1_HUMAN
5-24
2
A:5-24
B:5-24
3
BH3
PS01259
Apoptosis regulator, Bcl-2 family BH3 motif signature.
B2CL1_HUMAN
86-100
2
A:86-100
B:86-100
4
BCL2_FAMILY
PS50062
BCL2-like apoptosis inhibitors family profile.
B2CL1_HUMAN
90-190
2
A:90-190
B:90-190
5
BH1
PS01080
Apoptosis regulator, Bcl-2 family BH1 motif signature.
B2CL1_HUMAN
130-148
2
A:130-148
B:130-148
6
BH2
PS01258
Apoptosis regulator, Bcl-2 family BH2 motif signature.
B2CL1_HUMAN
181-192
2
A:181-192
B:181-192
[
close PROSITE info
]
Exons
(2, 4)
Info
All Exons
Exon 1.3a (A:1-188 (gaps) | B:1-188 (gaps))
Exon 1.4c (A:189-196 | B:189-198)
View:
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All Exon Boundaries
1: Boundary -/1.3a
2: Boundary 1.3a/1.4c
3: Boundary 1.4c/-
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
1.3a
ENST00000376062
3a
ENSE00001469279
chr20:
30310400-30309458
943
B2CL1_HUMAN
1-188
188
2
A:1-188 (gaps)
B:1-188 (gaps)
188
188
1.4c
ENST00000376062
4c
ENSE00001469296
chr20:
30253889-30252255
1635
B2CL1_HUMAN
189-233
45
2
A:189-196
B:189-198
8
10
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d4c52a_ (A:)
1b: SCOP_d4c52b_ (B:)
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Protein Domains
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(
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Organisms
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(
)
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Toxins' membrane translocation domains
(135)
Superfamily
:
Bcl-2 inhibitors of programmed cell death
(113)
Family
:
Bcl-2 inhibitors of programmed cell death
(102)
Protein domain
:
automated matches
(33)
Human (Homo sapiens) [TaxId: 9606]
(31)
1a
d4c52a_
A:
1b
d4c52b_
B:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
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Protein
Nucleic
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
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Asymmetric Unit 1
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