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3O9V
Biol. Unit 3
Info
Asym.Unit (498 KB)
Biol.Unit 1 (489 KB)
Biol.Unit 2 (250 KB)
Biol.Unit 3 (248 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN DPP4 BOUND TO TAK-986
Authors
:
J. K. Yano, K. Aertgeerts
Date
:
04 Aug 10 (Deposition) - 09 Feb 11 (Release) - 08 Oct 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.75
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:
[
Gene Ontology, PubMed, Web (Google)
]
)
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, 10)
Info
All Hetero Components
1a: 5-(AMINOMETHYL)-2-METHYL-4-(4-METH... (10Ta)
1b: 5-(AMINOMETHYL)-2-METHYL-4-(4-METH... (10Tb)
1c: 5-(AMINOMETHYL)-2-METHYL-4-(4-METH... (10Tc)
1d: 5-(AMINOMETHYL)-2-METHYL-4-(4-METH... (10Td)
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)
2r: N-ACETYL-D-GLUCOSAMINE (NAGr)
2s: N-ACETYL-D-GLUCOSAMINE (NAGs)
2t: N-ACETYL-D-GLUCOSAMINE (NAGt)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
10T
2
Ligand/Ion
5-(AMINOMETHYL)-2-METHYL-4-(4-METHYLPHENYL)-6-(2-METHYLPROPYL)PYRIDINE-3-CARBOXIC ACID
2
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(10, 10)
Info
All Sites
01: BC6 (SOFTWARE)
02: BC7 (SOFTWARE)
03: BC8 (SOFTWARE)
04: BC9 (SOFTWARE)
05: CC1 (SOFTWARE)
06: CC2 (SOFTWARE)
07: CC3 (SOFTWARE)
08: CC4 (SOFTWARE)
09: CC5 (SOFTWARE)
10: CC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
BC6
SOFTWARE
ARG C:125 , GLU C:205 , GLU C:206 , TYR C:547 , SER C:630 , VAL C:656 , TYR C:662 , TYR C:666 , HOH C:806
BINDING SITE FOR RESIDUE 10T C 1
02
BC7
SOFTWARE
ARG C:147 , ILE C:148 , ASN C:150 , HOH C:807 , HOH C:827
BINDING SITE FOR RESIDUE NAG C 1501
03
BC8
SOFTWARE
ASN C:229 , THR C:231 , GLU C:232 , NAG C:2292
BINDING SITE FOR RESIDUE NAG C 2291
04
BC9
SOFTWARE
GLU C:232 , NAG C:2291
BINDING SITE FOR RESIDUE NAG C 2292
05
CC1
SOFTWARE
TRP C:187 , ASN C:281
BINDING SITE FOR RESIDUE NAG C 2811
06
CC2
SOFTWARE
ARG D:125 , GLU D:205 , GLU D:206 , ARG D:358 , TYR D:547 , SER D:630 , VAL D:656 , TYR D:662 , TYR D:666 , HIS D:740
BINDING SITE FOR RESIDUE 10T D 1
07
CC3
SOFTWARE
ASN D:150 , HOH D:826
BINDING SITE FOR RESIDUE NAG D 1501
08
CC4
SOFTWARE
ASN D:229 , THR D:231 , GLU D:232 , LYS D:267 , NAG D:2292
BINDING SITE FOR RESIDUE NAG D 2291
09
CC5
SOFTWARE
GLU D:232 , HOH D:868 , NAG D:2291
BINDING SITE FOR RESIDUE NAG D 2292
10
CC6
SOFTWARE
TRP D:187 , ASN D:281 , HOH D:846
BINDING SITE FOR RESIDUE NAG D 2811
[
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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 (C:605-635,D: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
-
-
C:605-635
D: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_d3o9va1 (A:40-508)
1b: SCOP_d3o9vb1 (B:34-508)
1c: SCOP_d3o9vc1 (C:40-508)
1d: SCOP_d3o9vd1 (D:40-508)
2a: SCOP_d3o9va2 (A:509-766)
2b: SCOP_d3o9vb2 (B:509-766)
2c: SCOP_d3o9vc2 (C:509-766)
2d: SCOP_d3o9vd2 (D:509-766)
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)
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)
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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
d3o9va1
A:40-508
1b
d3o9vb1
B:34-508
1c
d3o9vc1
C:40-508
1d
d3o9vd1
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
d3o9va2
A:509-766
2b
d3o9vb2
B:509-766
2c
d3o9vc2
C:509-766
2d
d3o9vd2
D:509-766
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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
(2, 8)
Info
all PFAM domains
1a: PFAM_Peptidase_S9_3o9vD01 (D:559-765)
1b: PFAM_Peptidase_S9_3o9vD02 (D:559-765)
1c: PFAM_Peptidase_S9_3o9vD03 (D:559-765)
1d: PFAM_Peptidase_S9_3o9vD04 (D:559-765)
2a: PFAM_DPPIV_N_3o9vD05 (D:108-479)
2b: PFAM_DPPIV_N_3o9vD06 (D:108-479)
2c: PFAM_DPPIV_N_3o9vD07 (D:108-479)
2d: PFAM_DPPIV_N_3o9vD08 (D:108-479)
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Clans
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)
Organisms
(
)
(
)
Clan
:
AB_hydrolase
(347)
Family
:
Peptidase_S9
(57)
Homo sapiens (Human)
(33)
1a
Peptidase_S9-3o9vD01
D:559-765
1b
Peptidase_S9-3o9vD02
D:559-765
1c
Peptidase_S9-3o9vD03
D:559-765
1d
Peptidase_S9-3o9vD04
D:559-765
Clan
:
Beta_propeller
(192)
Family
:
DPPIV_N
(38)
Homo sapiens (Human)
(33)
2a
DPPIV_N-3o9vD05
D:108-479
2b
DPPIV_N-3o9vD06
D:108-479
2c
DPPIV_N-3o9vD07
D:108-479
2d
DPPIV_N-3o9vD08
D:108-479
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Asym.Unit (498 KB)
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