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Biol. Unit 1
Info
Asym.Unit (68 KB)
Biol.Unit 1 (247 KB)
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(1)
Title
:
DISCOVERY OF NOVEL CYANAMIDE-BASED INHIBITORS OF CATHEPSIN C
Authors
:
B. Zhao, D. Laine
Date
:
22 Oct 10 (Deposition) - 26 Oct 11 (Release) - 26 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A
Biol. Unit 1: A (4x)
Keywords
:
Two Domains, Cystein Protease, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Laine, M. Palovich, P. Mccleland, E. Petitjean, I. Delhom, H. Xie, J. Deng, G. Lin, R. Davis, A. Jolit, N. Nevins, J. Villa, J. Schneck
Discovery Of Novel Cyanamide-Based Inhibitors Of Cathepsin
To Be Published
[
close entry info
]
Hetero Components
(2, 20)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: 2,5-DIBROMO-N-{(3R,5S)-1-[(Z)-IMIN... (LXVa)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
LXV
4
Ligand/Ion
2,5-DIBROMO-N-{(3R,5S)-1-[(Z)-IMINOMETHYL]-5-METHYLPYRROLIDIN-3-YL}BENZENESULFONAMIDE
3
NAG
16
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
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:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:1 , TYR A:64 , GLN A:228 , GLY A:232 , CYS A:234 , GLY A:276 , GLY A:277 , PHE A:278 , PRO A:279 , THR A:379 , ASN A:380 , HOH A:716
BINDING SITE FOR RESIDUE LXV A 442
2
AC2
SOFTWARE
LEU A:54 , PHE A:206 , LEU A:207 , THR A:209 , ILE A:219 , ASN A:252 , NAG A:602
BINDING SITE FOR RESIDUE NAG A 601
3
AC3
SOFTWARE
NAG A:601
BINDING SITE FOR RESIDUE NAG A 602
4
AC4
SOFTWARE
ASN A:95 , HOH A:683
BINDING SITE FOR RESIDUE NAG A 603
5
AC5
SOFTWARE
ASN A:5 , ASN A:65 , LEU A:378 , HOH A:536
BINDING SITE FOR RESIDUE NAG A 604
6
AC6
SOFTWARE
PHE A:278 , PRO A:279 , TYR A:280 , TYR A:323 , VAL A:431
BINDING SITE FOR RESIDUE CL A 443
[
close Site info
]
SAPs(SNPs)/Variants
(29, 116)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_016933 (W15S, chain A, )
02: VAR_016934 (H103P, chain A, )
03: VAR_019036 (V105E, chain A, )
04: VAR_019037 (G115R, chain A, )
05: VAR_019038 (D212Y, chain A, )
06: VAR_009541 (V225F, chain A, )
07: VAR_009542 (Q228L, chain A, )
08: VAR_019039 (R248H, chain A, )
09: VAR_009543 (R248P, chain A, )
10: VAR_016935 (Q262R, chain A, )
11: VAR_019040 (C267Y, chain A, )
12: VAR_039686 (Y270H, chain A, )
13: VAR_019041 (G276D, chain A, )
14: VAR_019042 (G276S, chain A, )
15: VAR_009544 (G277S, chain A, )
16: VAR_019043 (G277V, chain A, )
17: VAR_019044 (Y280N, chain A, )
18: VAR_019045 (Q288R, chain A, )
19: VAR_019046 (E295G, chain A, )
20: VAR_009545 (R315C, chain A, )
21: VAR_016944 (Y316C, chain A, )
22: VAR_009546 (Y323C, chain A, )
23: VAR_016945 (E377K, chain A, )
24: VAR_027249 (H381N, chain A, )
25: VAR_027250 (H381R, chain A, )
26: VAR_019047 (Y388C, chain A, )
27: VAR_016936 (W405C, chain A, )
28: VAR_019048 (E423G, chain A, )
29: VAR_016946 (I429V, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_016933
W
39
S
CATC_HUMAN
Disease (PLS)
---
A
W
15
S
02
UniProt
VAR_016934
H
127
P
CATC_HUMAN
Disease (PLS)
---
A
H
103
P
03
UniProt
VAR_019036
V
129
E
CATC_HUMAN
Disease (PLS)
---
A
V
105
E
04
UniProt
VAR_019037
G
139
R
CATC_HUMAN
Disease (PLS)
---
A
G
115
R
05
UniProt
VAR_019038
D
236
Y
CATC_HUMAN
Disease (PLS)
---
A
D
212
Y
06
UniProt
VAR_009541
V
249
F
CATC_HUMAN
Disease (PLS)
---
A
V
225
F
07
UniProt
VAR_009542
Q
252
L
CATC_HUMAN
Disease (PLS)
---
A
Q
228
L
08
UniProt
VAR_019039
R
272
H
CATC_HUMAN
Disease (PLS)
---
A
R
248
H
09
UniProt
VAR_009543
R
272
P
CATC_HUMAN
Disease (PLS)
---
A
R
248
P
10
UniProt
VAR_016935
Q
286
R
CATC_HUMAN
Disease (PLS)
---
A
Q
262
R
11
UniProt
VAR_019040
C
291
Y
CATC_HUMAN
Disease (PLS)
---
A
C
267
Y
12
UniProt
VAR_039686
Y
294
H
CATC_HUMAN
Disease (PLS)
---
A
Y
270
H
13
UniProt
VAR_019041
G
300
D
CATC_HUMAN
Disease (PLS)
---
A
G
276
D
14
UniProt
VAR_019042
G
300
S
CATC_HUMAN
Disease (PLS)
---
A
G
276
S
15
UniProt
VAR_009544
G
301
S
CATC_HUMAN
Disease (PLS)
---
A
G
277
S
16
UniProt
VAR_019043
G
301
V
CATC_HUMAN
Disease (PLS)
---
A
G
277
V
17
UniProt
VAR_019044
Y
304
N
CATC_HUMAN
Disease (PLS)
---
A
Y
280
N
18
UniProt
VAR_019045
Q
312
R
CATC_HUMAN
Disease (PLS)
---
A
Q
288
R
19
UniProt
VAR_019046
E
319
G
CATC_HUMAN
Disease (PLS)
---
A
E
295
G
20
UniProt
VAR_009545
R
339
C
CATC_HUMAN
Disease (PLS)
---
A
R
315
C
21
UniProt
VAR_016944
Y
340
C
CATC_HUMAN
Disease (PLS)
---
A
Y
316
C
22
UniProt
VAR_009546
Y
347
C
CATC_HUMAN
Disease (AP1)
---
A
Y
323
C
23
UniProt
VAR_016945
E
401
K
CATC_HUMAN
Polymorphism
---
A
E
377
K
24
UniProt
VAR_027249
H
405
N
CATC_HUMAN
Disease (PLS)
---
A
H
381
N
25
UniProt
VAR_027250
H
405
R
CATC_HUMAN
Disease (PLS)
151269219
A
H
381
R
26
UniProt
VAR_019047
Y
412
C
CATC_HUMAN
Disease (AP1)
28937571
A
Y
388
C
27
UniProt
VAR_016936
W
429
C
CATC_HUMAN
Disease (PLS)
---
A
W
405
C
28
UniProt
VAR_019048
E
447
G
CATC_HUMAN
Disease (PLS)
---
A
E
423
G
29
UniProt
VAR_016946
I
453
V
CATC_HUMAN
Polymorphism
3888798
A
I
429
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 12)
Info
All PROSITE Patterns/Profiles
1: THIOL_PROTEASE_CYS (A:228-239)
2: THIOL_PROTEASE_HIS (A:379-389)
3: THIOL_PROTEASE_ASN (A:398-417)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THIOL_PROTEASE_CYS
PS00139
Eukaryotic thiol (cysteine) proteases cysteine active site.
CATC_HUMAN
252-263
4
A:228-239
2
THIOL_PROTEASE_HIS
PS00639
Eukaryotic thiol (cysteine) proteases histidine active site.
CATC_HUMAN
403-413
4
A:379-389
3
THIOL_PROTEASE_ASN
PS00640
Eukaryotic thiol (cysteine) proteases asparagine active site.
CATC_HUMAN
422-441
4
A:398-417
[
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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3pdfa1 (A:1-118)
2a: SCOP_d3pdfa2 (A:206-441)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Streptavidin-like
(225)
Superfamily
:
Dipeptidyl peptidase I (cathepsin C), exclusion domain
(9)
Family
:
automated matches
(1)
Protein domain
:
automated matches
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d3pdfa1
A:1-118
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cysteine proteinases
(392)
Superfamily
:
Cysteine proteinases
(392)
Family
:
Papain-like
(200)
Protein domain
:
automated matches
(30)
Human (Homo sapiens) [TaxId: 9606]
(7)
2a
d3pdfa2
A:206-441
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
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)
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Nucleic
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Asymmetric Unit 1
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