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3OPM
Biol. Unit 2
Info
Asym.Unit (1022 KB)
Biol.Unit 1 (1013 KB)
Biol.Unit 2 (511 KB)
Biol.Unit 3 (509 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN DPP4 BOUND TO TAK-294
Authors
:
J. K. Yano, K. Aertgeerts
Date
:
01 Sep 10 (Deposition) - 19 Oct 11 (Release) - 19 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.72
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B (1x)
Biol. Unit 3: C,D (1x)
Keywords
:
Protease And 8-Bladed Beta-Propeller Domain, Aminopeptidase, Cell Membrane, Glycoprotein, Hydrolase, Membrane, Protease, Secreted, Serine Protease, Signal-Anchor, Transmembrane, Signaling Protein, Hydrolase-Hydrolase Inhibitor, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Banno, Y. Miyamoto, M. Sasaki, S. Oi, T. Asakawa, O. Kataoka, K. Takeuchi, N. Suzuki, K. Ikedo, T. Kosaka, S. Tsubotani, A. Tani, M. Funami, M. Tawada, Y. Yamamoto, K. Aertgeerts, J. Yano, H. Maezaki
Identification Of 3-Aminomethyl-1, 2-Dihydro-4-Phenyl-1-Isoquinolones: A New Class Of Potent, Selective, And Orally Active Non-Peptide Dipeptidyl Peptidase Iv Inhibitors That Form A Unique Interaction With Lys554.
Bioorg. Med. Chem. V. 19 4953 2011
[
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Hetero Components
(2, 13)
Info
All Hetero Components
1a: 2-{[3-(AMINOMETHYL)-2-(2-METHYLPRO... (LUIa)
1b: 2-{[3-(AMINOMETHYL)-2-(2-METHYLPRO... (LUIb)
1c: 2-{[3-(AMINOMETHYL)-2-(2-METHYLPRO... (LUIc)
1d: 2-{[3-(AMINOMETHYL)-2-(2-METHYLPRO... (LUId)
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)
2g: N-ACETYL-D-GLUCOSAMINE (NAGg)
2h: N-ACETYL-D-GLUCOSAMINE (NAGh)
2i: N-ACETYL-D-GLUCOSAMINE (NAGi)
2j: N-ACETYL-D-GLUCOSAMINE (NAGj)
2k: N-ACETYL-D-GLUCOSAMINE (NAGk)
2l: N-ACETYL-D-GLUCOSAMINE (NAGl)
2m: N-ACETYL-D-GLUCOSAMINE (NAGm)
2n: N-ACETYL-D-GLUCOSAMINE (NAGn)
2o: N-ACETYL-D-GLUCOSAMINE (NAGo)
2p: N-ACETYL-D-GLUCOSAMINE (NAGp)
2q: N-ACETYL-D-GLUCOSAMINE (NAGq)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
LUI
2
Ligand/Ion
2-{[3-(AMINOMETHYL)-2-(2-METHYLPROPYL)-1-OXO-4-PHENYL-1,2-DIHYDROISOQUINOLIN-6-YL]OXY}ACETAMIDE
2
NAG
11
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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Sites
(13, 13)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:1 , ARG A:125 , GLU A:205 , GLU A:206 , PHE A:357 , TYR A:547 , TRP A:629 , TYR A:662 , TYR A:666 , HOH A:789
BINDING SITE FOR RESIDUE LUI A 800
02
AC2
SOFTWARE
ASN A:150 , HOH A:816 , HOH A:840
BINDING SITE FOR RESIDUE NAG A 1501
03
AC3
SOFTWARE
ASN A:219 , THR A:221 , GLN A:308 , GLU A:309 , HOH A:889
BINDING SITE FOR RESIDUE NAG A 2191
04
AC4
SOFTWARE
ILE A:194 , ASN A:229 , THR A:231 , GLU A:232 , NAG A:2292
BINDING SITE FOR RESIDUE NAG A 2291
05
AC5
SOFTWARE
THR A:231 , GLU A:232 , HOH A:836 , NAG A:2291
BINDING SITE FOR RESIDUE NAG A 2292
06
AC6
SOFTWARE
ASN A:281 , HOH A:866
BINDING SITE FOR RESIDUE NAG A 2811
07
AC7
SOFTWARE
ILE A:319 , ASN A:321 , SER A:349 , THR A:350 , ARG A:596 , HOH A:869
BINDING SITE FOR RESIDUE NAG A 3211
08
AC8
SOFTWARE
HOH B:22 , GLU B:205 , GLU B:206 , SER B:209 , PHE B:357 , TYR B:547 , LYS B:554 , TRP B:629 , SER B:630 , TYR B:631 , TYR B:662 , TYR B:666 , HOH B:814 , HOH B:815
BINDING SITE FOR RESIDUE LUI B 800
09
AC9
SOFTWARE
ASN B:85 , HOH B:818 , HOH B:874
BINDING SITE FOR RESIDUE NAG B 901
10
BC1
SOFTWARE
ARG B:147 , ILE B:148 , ASN B:150 , HOH B:826 , HOH B:827 , HOH B:834
BINDING SITE FOR RESIDUE NAG B 1501
11
BC2
SOFTWARE
ILE B:194 , ASN B:229 , THR B:231 , GLU B:232
BINDING SITE FOR RESIDUE NAG B 2291
12
BC3
SOFTWARE
TRP B:187 , ASN B:281 , HOH B:821 , HOH B:891
BINDING SITE FOR RESIDUE NAG B 2811
13
BC4
SOFTWARE
ILE B:319 , ASN B:321 , TYR B:322 , ARG B:596 , HOH B:792 , HOH B:883
BINDING SITE FOR RESIDUE NAG B 3211
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PRO_ENDOPEP_SER (A:605-635,B:605-635)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PRO_ENDOPEP_SER
PS00708
Prolyl endopeptidase family serine active site.
DPP4_HUMAN
605-635
2
A:605-635
B:605-635
-
-
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Exons
(0, 0)
Info
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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, 8)
Info
All SCOP Domains
1a: SCOP_d3opma1 (A:40-508)
1b: SCOP_d3opmb1 (B:34-508)
1c: SCOP_d3opmc1 (C:40-508)
1d: SCOP_d3opmd1 (D:40-508)
2a: SCOP_d3opma2 (A:509-766)
2b: SCOP_d3opmb2 (B:509-766)
2c: SCOP_d3opmc2 (C:509-766)
2d: SCOP_d3opmd2 (D:509-766)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
8-bladed beta-propeller
(135)
Superfamily
:
DPP6 N-terminal domain-like
(99)
Family
:
DPP6 N-terminal domain-like
(99)
Protein domain
:
Dipeptidyl peptidase IV/CD26, N-terminal domain
(88)
Human (Homo sapiens) [TaxId: 9606]
(80)
1a
d3opma1
A:40-508
1b
d3opmb1
B:34-508
1c
d3opmc1
C:40-508
1d
d3opmd1
D:40-508
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
alpha/beta-Hydrolases
(971)
Superfamily
:
alpha/beta-Hydrolases
(971)
Family
:
automated matches
(184)
Protein domain
:
automated matches
(184)
Human (Homo sapiens) [TaxId: 9606]
(42)
2a
d3opma2
A:509-766
2b
d3opmb2
B:509-766
2c
d3opmc2
C:509-766
2d
d3opmd2
D:509-766
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
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Sorry, no Info available
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (1022 KB)
Header - Asym.Unit
Biol.Unit 1 (1013 KB)
Header - Biol.Unit 1
Biol.Unit 2 (511 KB)
Header - Biol.Unit 2
Biol.Unit 3 (509 KB)
Header - Biol.Unit 3
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