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1Y8J
Asym. Unit
Info
Asym.Unit (125 KB)
Biol.Unit 1 (120 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN NEP COMPLEXED WITH AN IMIDAZO[4,5-C]PYRIDINE INHIBITOR
Authors
:
S. Sahli, B. Frank, W. B. Schweizer, F. Diederich, D. Blum-Kaelin, J. D. H. J. Bohm, C. Oefner, G. E. Dale
Date
:
13 Dec 04 (Deposition) - 07 Jun 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Lt1_6, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Sahli, B. Frank, W. B. Schweizer, F. Diederich, D. Blum-Kaelin, J. D. Aebi, H. J. Bohm, C. Oefner, G. E. Dale
Second-Generation Inhibitors For The Metalloprotease Neprilysin Based On Bicyclic Heteroaromatic Scaffolds: Synthesis, Biological Activity, And X-Ray Crystal Structure Analysis
Helv. Chim. Acta V. 88 731 2005
[
close entry info
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Hetero Components
(4, 6)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3a: 2-[(1S)-1-BENZYL-2-SULFANYLETHYL]-... (STSa)
4a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
1
Ligand/Ion
ACETATE ION
2
NAG
3
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
STS
1
Ligand/Ion
2-[(1S)-1-BENZYL-2-SULFANYLETHYL]-1H-IMIDAZO[4,5-C]PYRIDIN-5-IUM
4
ZN
1
Ligand/Ion
ZINC ION
[
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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:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:144 , ALA A:147
BINDING SITE FOR RESIDUE NAG A 752
2
AC2
SOFTWARE
ASN A:324 , ASN A:327 , GLU A:328 , HOH A:1046 , HOH A:1047
BINDING SITE FOR RESIDUE NAG A 753
3
AC3
SOFTWARE
TYR A:623 , GLY A:626 , ASN A:627
BINDING SITE FOR RESIDUE NAG A 754
4
AC4
SOFTWARE
HIS A:583 , HIS A:587 , GLU A:646 , STS A:900
BINDING SITE FOR RESIDUE ZN A 800
5
AC5
SOFTWARE
VAL A:198 , LEU A:199 , ARG A:222 , LEU A:223 , GLU A:279 , ILE A:282 , ARG A:373
BINDING SITE FOR RESIDUE ACT A 801
6
AC6
SOFTWARE
ARG A:110 , ASN A:542 , ALA A:543 , MET A:579 , HIS A:583 , GLU A:584 , GLU A:646 , TRP A:693 , HIS A:711 , ARG A:717 , ZN A:800
BINDING SITE FOR RESIDUE STS A 900
[
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]
SAPs(SNPs)/Variants
(6, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_077685 (C142Y, chain A, )
2: VAR_077686 (Y346C, chain A, )
3: VAR_077687 (A347P, chain A, )
4: VAR_077689 (A421D, chain A, )
5: VAR_077690 (Y496H, chain A, )
6: VAR_077691 (C620R, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_077685
C
143
Y
NEP_HUMAN
Disease (SCA43)
879255651
A
C
142
Y
2
UniProt
VAR_077686
Y
347
C
NEP_HUMAN
Disease (CMT2T)
138218277
A
Y
346
C
3
UniProt
VAR_077687
A
348
P
NEP_HUMAN
Unclassified (CMT2T)
199567914
A
A
347
P
4
UniProt
VAR_077689
A
422
D
NEP_HUMAN
Disease (CMT2T)
777476150
A
A
421
D
5
UniProt
VAR_077690
Y
497
H
NEP_HUMAN
Polymorphism
200308207
A
Y
496
H
6
UniProt
VAR_077691
C
621
R
NEP_HUMAN
Disease (CMT2T)
879253752
A
C
620
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:580-589)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ZINC_PROTEASE
PS00142
Neutral zinc metallopeptidases, zinc-binding region signature.
NEP_HUMAN
581-590
1
A:580-589
[
close PROSITE info
]
Exons
(21, 21)
Info
All Exons
Exon 1.10a (A:54-65)
Exon 1.13c (A:65-119)
Exon 1.14 (A:119-146)
Exon 1.15b (A:146-178)
Exon 1.16 (A:178-217)
Exon 1.17b (A:218-239)
Exon 1.18 (A:240-284)
Exon 1.19 (A:285-318)
Exon 1.20 (A:319-364)
Exon 1.21 (A:364-395)
Exon 1.22 (A:396-438)
Exon 1.23 (A:439-471)
Exon 1.24 (A:472-498)
Exon 1.25 (A:499-533)
Exon 1.26 (A:533-553)
Exon 1.27 (A:553-593)
Exon 1.28 (A:593-637)
Exon 1.29a (A:638-659)
Exon 1.30b (A:660-691)
Exon 1.31 (A:692-717)
Exon 1.32a (A:717-749)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.9b/1.10a
02: Boundary 1.10a/1.13c
03: Boundary 1.13c/1.14
04: Boundary 1.14/1.15b
05: Boundary 1.15b/1.16
06: Boundary 1.16/1.17b
07: Boundary 1.17b/1.18
08: Boundary 1.18/1.19
09: Boundary 1.19/1.20
10: Boundary 1.20/1.21
11: Boundary 1.21/1.22
12: Boundary 1.22/1.23
13: Boundary 1.23/1.24
14: Boundary 1.24/1.25
15: Boundary 1.25/1.26
16: Boundary 1.26/1.27
17: Boundary 1.27/1.28
18: Boundary 1.28/1.29a
19: Boundary 1.29a/1.30b
20: Boundary 1.30b/1.31
21: Boundary 1.31/1.32a
22: Boundary 1.32a/-
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
1.4d
ENST00000360490
4d
ENSE00001513376
chr3:
154798188-154798255
68
NEP_HUMAN
-
0
0
-
-
1.9b
ENST00000360490
9b
ENSE00002152527
chr3:
154801947-154802116
170
NEP_HUMAN
1-54
54
0
-
-
1.10a
ENST00000360490
10a
ENSE00001019489
chr3:
154802848-154802883
36
NEP_HUMAN
54-66
13
1
A:54-65
12
1.13c
ENST00000360490
13c
ENSE00002199839
chr3:
154832783-154832944
162
NEP_HUMAN
66-120
55
1
A:65-119
55
1.14
ENST00000360490
14
ENSE00000934032
chr3:
154834268-154834348
81
NEP_HUMAN
120-147
28
1
A:119-146
28
1.15b
ENST00000360490
15b
ENSE00000934033
chr3:
154834453-154834548
96
NEP_HUMAN
147-179
33
1
A:146-178
33
1.16
ENST00000360490
16
ENSE00000934034
chr3:
154834657-154834775
119
NEP_HUMAN
179-218
40
1
A:178-217
40
1.17b
ENST00000360490
17b
ENSE00000934035
chr3:
154836535-154836600
66
NEP_HUMAN
219-240
22
1
A:218-239
22
1.18
ENST00000360490
18
ENSE00001019488
chr3:
154855891-154856025
135
NEP_HUMAN
241-285
45
1
A:240-284
45
1.19
ENST00000360490
19
ENSE00000934036
chr3:
154857980-154858081
102
NEP_HUMAN
286-319
34
1
A:285-318
34
1.20
ENST00000360490
20
ENSE00000934037
chr3:
154859780-154859916
137
NEP_HUMAN
320-365
46
1
A:319-364
46
1.21
ENST00000360490
21
ENSE00000934038
chr3:
154860026-154860119
94
NEP_HUMAN
365-396
32
1
A:364-395
32
1.22
ENST00000360490
22
ENSE00000934039
chr3:
154861232-154861360
129
NEP_HUMAN
397-439
43
1
A:396-438
43
1.23
ENST00000360490
23
ENSE00000934040
chr3:
154862148-154862246
99
NEP_HUMAN
440-472
33
1
A:439-471
33
1.24
ENST00000360490
24
ENSE00000934041
chr3:
154864933-154865013
81
NEP_HUMAN
473-499
27
1
A:472-498
27
1.25
ENST00000360490
25
ENSE00000779819
chr3:
154866339-154866442
104
NEP_HUMAN
500-534
35
1
A:499-533
35
1.26
ENST00000360490
26
ENSE00000779818
chr3:
154878179-154878237
59
NEP_HUMAN
534-554
21
1
A:533-553
21
1.27
ENST00000360490
27
ENSE00000779817
chr3:
154884691-154884810
120
NEP_HUMAN
554-594
41
1
A:553-593
41
1.28
ENST00000360490
28
ENSE00000779816
chr3:
154886281-154886414
134
NEP_HUMAN
594-638
45
1
A:593-637
45
1.29a
ENST00000360490
29a
ENSE00000779815
chr3:
154886521-154886586
66
NEP_HUMAN
639-660
22
1
A:638-659
22
1.30b
ENST00000360490
30b
ENSE00000779814
chr3:
154889906-154890001
96
NEP_HUMAN
661-692
32
1
A:660-691
32
1.31
ENST00000360490
31
ENSE00000779812
chr3:
154890325-154890401
77
NEP_HUMAN
693-718
26
1
A:692-717
26
1.32a
ENST00000360490
32a
ENSE00001182656
chr3:
154898149-154898277
129
NEP_HUMAN
718-750
33
1
A:717-749
33
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1y8ja_ (A:)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Zincin-like
(701)
Superfamily
:
Metalloproteases (zincins), catalytic domain
(647)
Family
:
Neutral endopeptidase (neprilysin)
(7)
Protein domain
:
Neutral endopeptidase (neprilysin)
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d1y8ja_
A:
[
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1y8jA01 (A:54-103,A:431-482,A:530-749)
2a: CATH_1y8jA02 (A:104-430,A:483-529)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Collagenase (Catalytic Domain)
(236)
Homologous Superfamily
:
Collagenase (Catalytic Domain)
(234)
Human (Homo sapiens)
(153)
1a
1y8jA01
A:54-103,A:431-482,A:530-749
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Neutral endopeptidase; domain 2
(6)
Homologous Superfamily
:
Neutral endopeptidase , domain2
(6)
Human (Homo sapiens)
(6)
2a
1y8jA02
A:104-430,A:483-529
[
close CATH info
]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Peptidase_M13_1y8jA01 (A:542-748)
2a: PFAM_Peptidase_M13_N_1y8jA02 (A:79-482)
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Clans
(
)
(
)
Families
(
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(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M13
(6)
Homo sapiens (Human)
(6)
1a
Peptidase_M13-1y8jA01
A:542-748
Clan
:
no clan defined [family: Peptidase_M13_N]
(6)
Family
:
Peptidase_M13_N
(6)
Homo sapiens (Human)
(6)
2a
Peptidase_M13_N-1y8jA02
A:79-482
[
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Asymmetric Unit 1
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