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3O95
Biol. Unit 2
Info
Asym.Unit (502 KB)
Biol.Unit 1 (493 KB)
Biol.Unit 2 (254 KB)
Biol.Unit 3 (247 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN DPP4 BOUND TO TAK-100
Authors
:
J. K. Yano, K. Aertgeerts
Date
:
03 Aug 10 (Deposition) - 26 Jan 11 (Release) - 08 Oct 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.85
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, Signaling Protein, Hydrolase, Signaling Protein-Inhibitor Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
Y. Miyamoto, Y. Banno, T. Yamashita, T. Fujimoto, S. Oi, Y. Moritoh, T. Asakawa, O. Kataoka, H. Yashiro, K. Takeuchi, N. Suzuki, K. Ikedo, T. Kosaka, S. Tsubotani, A. Tani, M. Sasaki, M. Funami, M. Amano, Y. Yamamoto, K. Aertgeerts, J. Yano, H. Maezaki
Discovery Of A 3-Pyridylacetic Acid Derivative (Tak-100) As A Potent, Selective And Orally Active Dipeptidyl Peptidase Iv (Dpp-4) Inhibitor.
J. Med. Chem. V. 53 3517 2011
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Hetero Components
(2, 19)
Info
All Hetero Components
1a: [5-(AMINOMETHYL)-6-(2,2-DIMETHYLPR... (01Ta)
1b: [5-(AMINOMETHYL)-6-(2,2-DIMETHYLPR... (01Tb)
1c: [5-(AMINOMETHYL)-6-(2,2-DIMETHYLPR... (01Tc)
1d: [5-(AMINOMETHYL)-6-(2,2-DIMETHYLPR... (01Td)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
2ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
2ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
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)
2r: N-ACETYL-D-GLUCOSAMINE (NAGr)
2s: N-ACETYL-D-GLUCOSAMINE (NAGs)
2t: N-ACETYL-D-GLUCOSAMINE (NAGt)
2u: N-ACETYL-D-GLUCOSAMINE (NAGu)
2v: N-ACETYL-D-GLUCOSAMINE (NAGv)
2w: N-ACETYL-D-GLUCOSAMINE (NAGw)
2x: N-ACETYL-D-GLUCOSAMINE (NAGx)
2y: N-ACETYL-D-GLUCOSAMINE (NAGy)
2z: N-ACETYL-D-GLUCOSAMINE (NAGz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
01T
2
Ligand/Ion
[5-(AMINOMETHYL)-6-(2,2-DIMETHYLPROPYL)-2-ETHYL-4-(4-METHYLPHENYL)PYRIDIN-3-YL]ACETIC ACID
2
NAG
17
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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]
Sites
(19, 19)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:147 , ASN A:150 , HOH A:778 , HOH A:902 , NAG A:1502
BINDING SITE FOR RESIDUE NAG A 1501
02
AC2
SOFTWARE
NAG A:1501
BINDING SITE FOR RESIDUE NAG A 1502
03
AC3
SOFTWARE
ASN A:85 , SER A:86 , SER A:87 , NAG A:1504
BINDING SITE FOR RESIDUE NAG A 1503
04
AC4
SOFTWARE
NAG A:1503
BINDING SITE FOR RESIDUE NAG A 1504
05
AC5
SOFTWARE
ASN A:219 , THR A:221 , GLN A:308 , GLU A:309
BINDING SITE FOR RESIDUE NAG A 2191
06
AC6
SOFTWARE
ILE A:194 , ASN A:229 , THR A:231 , GLU A:232 , NAG A:2292
BINDING SITE FOR RESIDUE NAG A 2291
07
AC7
SOFTWARE
THR A:231 , HOH A:898 , NAG A:2291
BINDING SITE FOR RESIDUE NAG A 2292
08
AC8
SOFTWARE
TRP A:187 , ASN A:281 , NAG A:2812
BINDING SITE FOR RESIDUE NAG A 2811
09
AC9
SOFTWARE
NAG A:2811
BINDING SITE FOR RESIDUE NAG A 2812
10
BC1
SOFTWARE
ILE A:319 , ASN A:321 , SER A:349 , THR A:350 , HOH A:878
BINDING SITE FOR RESIDUE NAG A 3211
11
BC2
SOFTWARE
ARG A:125 , GLU A:205 , GLU A:206 , PHE A:357 , TYR A:547 , SER A:630 , VAL A:656 , TYR A:662 , TYR A:666 , VAL A:711 , HIS A:740 , HOH A:775 , HOH A:792
BINDING SITE FOR RESIDUE 01T A 1
12
BC3
SOFTWARE
ASN B:85 , SER B:87 , HOH B:829 , HOH B:839 , HOH B:849 , HOH B:877 , HOH B:885 , NAG B:902
BINDING SITE FOR RESIDUE NAG B 901
13
BC4
SOFTWARE
TYR B:83 , HOH B:849 , HOH B:853 , HOH B:885 , NAG B:901
BINDING SITE FOR RESIDUE NAG B 902
14
BC5
SOFTWARE
ARG B:147 , ILE B:148 , ASN B:150 , HOH B:838 , HOH B:854
BINDING SITE FOR RESIDUE NAG B 1501
15
BC6
SOFTWARE
ILE B:194 , ASN B:229 , THR B:231 , GLU B:232 , NAG B:2292
BINDING SITE FOR RESIDUE NAG B 2291
16
BC7
SOFTWARE
GLU B:232 , NAG B:2291
BINDING SITE FOR RESIDUE NAG B 2292
17
BC8
SOFTWARE
TRP B:187 , ASN B:281 , HOH B:842 , HOH B:869
BINDING SITE FOR RESIDUE NAG B 2811
18
BC9
SOFTWARE
ILE B:319 , ASN B:321 , SER B:349 , HOH B:862
BINDING SITE FOR RESIDUE NAG B 3211
19
CC1
SOFTWARE
ARG B:125 , GLU B:205 , GLU B:206 , SER B:209 , TYR B:547 , SER B:630 , VAL B:656 , TYR B:662 , TYR B:666 , HIS B:740 , HOH B:794
BINDING SITE FOR RESIDUE 01T B 1
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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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:
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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
All Exons
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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_d3o95a1 (A:40-508)
1b: SCOP_d3o95b1 (B:34-508)
1c: SCOP_d3o95c1 (C:41-508)
1d: SCOP_d3o95d1 (D:40-508)
2a: SCOP_d3o95a2 (A:509-766)
2b: SCOP_d3o95b2 (B:509-766)
2c: SCOP_d3o95c2 (C:509-766)
2d: SCOP_d3o95d2 (D:509-766)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d3o95a1
A:40-508
1b
d3o95b1
B:34-508
1c
d3o95c1
C:41-508
1d
d3o95d1
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
d3o95a2
A:509-766
2b
d3o95b2
B:509-766
2c
d3o95c2
C:509-766
2d
d3o95d2
D:509-766
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Peptidase_S9_3o95D01 (D:559-765)
1b: PFAM_Peptidase_S9_3o95D02 (D:559-765)
1c: PFAM_Peptidase_S9_3o95D03 (D:559-765)
1d: PFAM_Peptidase_S9_3o95D04 (D:559-765)
2a: PFAM_DPPIV_N_3o95D05 (D:108-479)
2b: PFAM_DPPIV_N_3o95D06 (D:108-479)
2c: PFAM_DPPIV_N_3o95D07 (D:108-479)
2d: PFAM_DPPIV_N_3o95D08 (D:108-479)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
AB_hydrolase
(347)
Family
:
Peptidase_S9
(57)
Homo sapiens (Human)
(33)
1a
Peptidase_S9-3o95D01
D:559-765
1b
Peptidase_S9-3o95D02
D:559-765
1c
Peptidase_S9-3o95D03
D:559-765
1d
Peptidase_S9-3o95D04
D:559-765
Clan
:
Beta_propeller
(192)
Family
:
DPPIV_N
(38)
Homo sapiens (Human)
(33)
2a
DPPIV_N-3o95D05
D:108-479
2b
DPPIV_N-3o95D06
D:108-479
2c
DPPIV_N-3o95D07
D:108-479
2d
DPPIV_N-3o95D08
D:108-479
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