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3WIY
Asym. Unit
Info
Asym.Unit (326 KB)
Biol.Unit 1 (56 KB)
Biol.Unit 2 (55 KB)
Biol.Unit 3 (55 KB)
Biol.Unit 4 (55 KB)
Biol.Unit 5 (57 KB)
Biol.Unit 6 (55 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MCL-1 IN COMPLEX WITH COMPOUND 10
Authors
:
S. Sogabe, S. Igaki, Y. Hayano
Date
:
26 Sep 13 (Deposition) - 27 Nov 13 (Release) - 12 Mar 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Keywords
:
Regulation, Apoptosis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Tanaka, K. Aikawa, G. Nishida, M. Homma, S. Sogabe, S. Igaki, Y. Hayano, T. Sameshima, I. Miyahisa, T. Kawamoto, M. Tawada, Y. Imai, M. Inazuka, N. Cho, Y. Imaeda, T. Ishikawa
Discovery Of Potent Mcl-1/Bcl-Xl Dual Inhibitors By Using A Hybridization Strategy Based On Structural Analysis Of Target Proteins.
J. Med. Chem. V. 56 9635 2013
[
close entry info
]
Hetero Components
(1, 6)
Info
All Hetero Components
1a: 7-(4-{[(4-{[(2R)-4-(DIMETHYLAMINO)... (LC6a)
1b: 7-(4-{[(4-{[(2R)-4-(DIMETHYLAMINO)... (LC6b)
1c: 7-(4-{[(4-{[(2R)-4-(DIMETHYLAMINO)... (LC6c)
1d: 7-(4-{[(4-{[(2R)-4-(DIMETHYLAMINO)... (LC6d)
1e: 7-(4-{[(4-{[(2R)-4-(DIMETHYLAMINO)... (LC6e)
1f: 7-(4-{[(4-{[(2R)-4-(DIMETHYLAMINO)... (LC6f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
LC6
6
Ligand/Ion
7-(4-{[(4-{[(2R)-4-(DIMETHYLAMINO)-1-(PHENYLSULFANYL)BUTAN-2-YL]AMINO}-3-NITROPHENYL)SULFONYL]CARBAMOYL}-2-METHYLPHENYL)-3-[3-(NAPHTHALEN-1-YLOXY)PROPYL]PYRAZOLO[1,5-A]PYRIDINE-2-CARBOXYLIC ACID
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:226 , ALA A:227 , PHE A:228 , GLY A:230 , LYS A:234 , LEU A:246 , MET A:250 , VAL A:253 , ARG A:263 , THR A:266 , LEU A:267 , PHE A:270 , GLU B:225 , THR B:226 , SER D:255 , ARG D:300
BINDING SITE FOR RESIDUE LC6 A 501
2
AC2
SOFTWARE
HIS B:224 , ALA B:227 , PHE B:228 , LEU B:235 , VAL B:253 , ARG B:263 , THR B:266 , LEU B:267 , PHE B:270 , LC6 D:501
BINDING SITE FOR RESIDUE LC6 B 501
3
AC3
SOFTWARE
GLU A:322 , HIS C:224 , LEU C:235 , MET C:250 , VAL C:253 , ARG C:263 , LEU C:267 , PHE C:270 , HOH C:913 , LC6 F:501 , HOH F:919
BINDING SITE FOR RESIDUE LC6 C 501
4
AC4
SOFTWARE
ARG B:263 , LC6 B:501 , HIS D:224 , ALA D:227 , PHE D:228 , MET D:250 , PHE D:254 , ARG D:263 , THR D:266 , LEU D:267 , PHE D:270 , GLY D:271 , ILE D:294 , HIS E:320
BINDING SITE FOR RESIDUE LC6 D 501
5
AC5
SOFTWARE
GLU C:225 , THR C:226 , HIS E:224 , THR E:226 , ALA E:227 , GLY E:230 , LYS E:234 , LEU E:235 , MET E:250 , ARG E:263 , THR E:266 , LEU E:267 , PHE E:270 , SER F:255 , ARG F:300
BINDING SITE FOR RESIDUE LC6 E 501
6
AC6
SOFTWARE
HIS A:320 , VAL C:258 , ARG C:263 , LC6 C:501 , ALA F:227 , LEU F:235 , MET F:250 , PHE F:254 , ARG F:263 , THR F:266 , LEU F:267 , PHE F:270 , GLY F:271
BINDING SITE FOR RESIDUE LC6 F 501
[
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SAPs(SNPs)/Variants
(3, 18)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_024021 (E173D, chain A/B/C/D/E/F, )
2: VAR_024022 (A227V, chain A/B/C/D/E/F, )
3: VAR_054157 (M231L, chain A/B/C/D/E/F, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_024021
E
173
D
MCL1_HUMAN
Polymorphism
2737820
A/B/C/D/E/F
E
173
D
2
UniProt
VAR_024022
A
227
V
MCL1_HUMAN
Polymorphism
11580946
A/B/C/D/E/F
A
227
V
3
UniProt
VAR_054157
M
231
L
MCL1_HUMAN
Polymorphism
---
A/B/C/D/E/F
M
231
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(4, 24)
Info
All PROSITE Patterns/Profiles
1: BH3 (A:209-223,B:209-223,C:209-223,D:20...)
2: BCL2_FAMILY (A:213-314,B:213-314,C:213-314,D:21...)
3: BH1 (A:253-272,B:253-272,C:253-272,D:25...)
4: BH2 (A:305-316,B:305-316,C:305-316,D:30...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BH3
PS01259
Apoptosis regulator, Bcl-2 family BH3 motif signature.
MCL1_HUMAN
209-223
6
A:209-223
B:209-223
C:209-223
D:209-223
E:209-223
F:209-223
2
BCL2_FAMILY
PS50062
BCL2-like apoptosis inhibitors family profile.
MCL1_HUMAN
213-314
6
A:213-314
B:213-314
C:213-314
D:213-314
E:213-314
F:213-314
3
BH1
PS01080
Apoptosis regulator, Bcl-2 family BH1 motif signature.
MCL1_HUMAN
253-272
6
A:253-272
B:253-272
C:253-272
D:253-272
E:253-272
F:253-272
4
BH2
PS01258
Apoptosis regulator, Bcl-2 family BH2 motif signature.
MCL1_HUMAN
305-316
6
A:305-316
B:305-316
C:305-316
D:305-316
E:305-316
F:305-316
[
close PROSITE info
]
Exons
(3, 18)
Info
All Exons
Exon 1.1a (A:172-230 | B:172-230 | C:172-230 ...)
Exon 1.2b (A:230-312 | B:230-312 | C:230-312 ...)
Exon 1.3d (A:313-323 | B:313-322 | C:313-321 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2b
3: Boundary 1.2b/1.3d
4: Boundary 1.3d/-
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
ENST00000369026
1a
ENSE00001152267
chr1:
150552066-150551319
748
MCL1_HUMAN
1-230
230
6
A:172-230
B:172-230
C:172-230
D:172-230
E:172-230
F:172-230
59
59
59
59
59
59
1.2b
ENST00000369026
2b
ENSE00000959746
chr1:
150550967-150550720
248
MCL1_HUMAN
230-312
83
6
A:230-312
B:230-312
C:230-312
D:230-312
E:230-312
F:230-312
83
83
83
83
83
83
1.3d
ENST00000369026
3d
ENSE00001696123
chr1:
150549967-150547032
2936
MCL1_HUMAN
313-350
38
6
A:313-323
B:313-322
C:313-321
D:313-321
E:313-323
F:313-321
11
10
9
9
11
9
[
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]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d3wiya_ (A:)
1b: SCOP_d3wiyb_ (B:)
1c: SCOP_d3wiyc_ (C:)
1d: SCOP_d3wiyd_ (D:)
1e: SCOP_d3wiye_ (E:)
1f: SCOP_d3wiyf_ (F:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
d3wiya_
A:
1b
d3wiyb_
B:
1c
d3wiyc_
C:
1d
d3wiyd_
D:
1e
d3wiye_
E:
1f
d3wiyf_
F:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
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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