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2ONC
Biol. Unit 1
Info
Asym.Unit (510 KB)
Biol.Unit 1 (257 KB)
Biol.Unit 2 (252 KB)
Biol.Unit 3 (251 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN DPP-4
Authors
:
J. Feng, Z. Zhang, M. B. Wallace, J. A. Stafford, S. W. Kaldor, D. B. Kasse M. Navre, L. Shi, R. J. Skene, T. Asakawa, K. Takeuchi, R. Xu, D. R. Webb, S. L. Gwaltney
Date
:
23 Jan 07 (Deposition) - 04 Mar 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.55
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: C,D (1x)
Keywords
:
Dpp4 Protein-Inhibitor Complex, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Feng, Z. Zhang, M. B. Wallace, J. A. Stafford, S. W. Kaldor, D. B. Kassel, M. Navre, L. Shi, R. J. Skene, T. Asakawa, K. Takeuchi, R. Xu, D. R. Webb, S. L. Gwaltney
Discovery Of Alogliptin: A Potent, Selective, Bioavailable, And Efficacious Inhibitor Of Dipeptidyl Peptidase Iv.
J. Med. Chem. V. 50 2297 2007
[
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Hetero Components
(2, 18)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
1f: N-ACETYL-D-GLUCOSAMINE (NAGf)
1g: N-ACETYL-D-GLUCOSAMINE (NAGg)
1h: N-ACETYL-D-GLUCOSAMINE (NAGh)
1i: N-ACETYL-D-GLUCOSAMINE (NAGi)
1j: N-ACETYL-D-GLUCOSAMINE (NAGj)
1k: N-ACETYL-D-GLUCOSAMINE (NAGk)
1l: N-ACETYL-D-GLUCOSAMINE (NAGl)
1m: N-ACETYL-D-GLUCOSAMINE (NAGm)
1n: N-ACETYL-D-GLUCOSAMINE (NAGn)
1o: N-ACETYL-D-GLUCOSAMINE (NAGo)
1p: N-ACETYL-D-GLUCOSAMINE (NAGp)
1q: N-ACETYL-D-GLUCOSAMINE (NAGq)
1r: N-ACETYL-D-GLUCOSAMINE (NAGr)
1s: N-ACETYL-D-GLUCOSAMINE (NAGs)
1t: N-ACETYL-D-GLUCOSAMINE (NAGt)
1u: N-ACETYL-D-GLUCOSAMINE (NAGu)
1v: N-ACETYL-D-GLUCOSAMINE (NAGv)
1w: N-ACETYL-D-GLUCOSAMINE (NAGw)
1x: N-ACETYL-D-GLUCOSAMINE (NAGx)
2a: 2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]... (SY1a)
2b: 2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]... (SY1b)
2c: 2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]... (SY1c)
2d: 2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]... (SY1d)
2e: 2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]... (SY1e)
2f: 2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]... (SY1f)
2g: 2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]... (SY1g)
2h: 2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]... (SY1h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
14
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
SY1
4
Ligand/Ion
2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]-4-OXOQUINAZOLIN-3(4H)-YL}METHYL)BENZONITRILE
[
close Hetero Component info
]
Sites
(14, 14)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC6 (SOFTWARE)
06: AC7 (SOFTWARE)
07: AC8 (SOFTWARE)
08: AC9 (SOFTWARE)
09: BC1 (SOFTWARE)
10: BC2 (SOFTWARE)
11: CC2 (SOFTWARE)
12: CC3 (SOFTWARE)
13: CC4 (SOFTWARE)
14: CC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:85 , SER A:86
BINDING SITE FOR RESIDUE NAG A 802
02
AC2
SOFTWARE
ASN A:150 , HOH A:1006
BINDING SITE FOR RESIDUE NAG A 803
03
AC3
SOFTWARE
ASN A:219 , THR A:221 , GLN A:308 , GLU A:309
BINDING SITE FOR RESIDUE NAG A 804
04
AC4
SOFTWARE
ASN A:281
BINDING SITE FOR RESIDUE NAG A 805
05
AC6
SOFTWARE
ILE A:319 , ASN A:321 , SER A:349
BINDING SITE FOR RESIDUE NAG A 807
06
AC7
SOFTWARE
ILE A:194 , ASN A:229 , THR A:231 , GLU A:232
BINDING SITE FOR RESIDUE NAG A 808
07
AC8
SOFTWARE
THR A:231
BINDING SITE FOR RESIDUE NAG A 809
08
AC9
SOFTWARE
TYR B:83 , ASN B:85
BINDING SITE FOR RESIDUE NAG B 802
09
BC1
SOFTWARE
ASN B:219 , THR B:221 , GLN B:308 , GLU B:309
BINDING SITE FOR RESIDUE NAG B 804
10
BC2
SOFTWARE
ILE B:194 , ASN B:229 , THR B:231 , GLU B:232
BINDING SITE FOR RESIDUE NAG B 805
11
CC2
SOFTWARE
ARG A:125 , GLU A:205 , GLU A:206 , TYR A:547 , SER A:630 , TYR A:631 , TYR A:662 , TYR A:666
BINDING SITE FOR RESIDUE SY1 A 800
12
CC3
SOFTWARE
GLN A:123 , GLU A:191 , ASP A:192 , LYS A:250 , THR A:251 , ARG A:253
BINDING SITE FOR RESIDUE SY1 A 801
13
CC4
SOFTWARE
ARG B:125 , GLU B:205 , GLU B:206 , TYR B:547 , TRP B:629 , SER B:630 , TYR B:631 , TYR B:662 , TYR B:666 , HOH B:908
BINDING SITE FOR RESIDUE SY1 B 800
14
CC5
SOFTWARE
GLN B:123 , GLU B:191 , ASP B:192 , LYS B:250 , ARG B:253
BINDING SITE FOR RESIDUE SY1 B 801
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
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
All Exons
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All Exon Boundaries
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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_d2onca1 (A:40-508)
1b: SCOP_d2oncb1 (B:36-508)
1c: SCOP_d2oncc1 (C:40-508)
1d: SCOP_d2oncd1 (D:40-508)
2a: SCOP_d2onca2 (A:509-766)
2b: SCOP_d2oncb2 (B:509-766)
2c: SCOP_d2oncc2 (C:509-766)
2d: SCOP_d2oncd2 (D:509-766)
View:
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)
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)
Folds
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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
d2onca1
A:40-508
1b
d2oncb1
B:36-508
1c
d2oncc1
C:40-508
1d
d2oncd1
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
d2onca2
A:509-766
2b
d2oncb2
B:509-766
2c
d2oncc2
C:509-766
2d
d2oncd2
D:509-766
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2oncA02 (A:509-766)
1b: CATH_2oncB02 (B:509-766)
1c: CATH_2oncC02 (C:509-766)
1d: CATH_2oncD02 (D:509-766)
2a: CATH_2oncD01 (D:40-508)
2b: CATH_2oncC01 (C:40-508)
2c: CATH_2oncA01 (A:40-508)
2d: CATH_2oncB01 (B:36-508)
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Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1820, no name defined]
(692)
Human (Homo sapiens)
(118)
1a
2oncA02
A:509-766
1b
2oncB02
B:509-766
1c
2oncC02
C:509-766
1d
2oncD02
D:509-766
Class
:
Mainly Beta
(13760)
Architecture
:
8 Propellor
(110)
Topology
:
Methanol Dehydrogenase; Chain A
(110)
Homologous Superfamily
:
[code=2.140.10.30, no name defined]
(74)
Human (Homo sapiens)
(59)
2a
2oncD01
D:40-508
2b
2oncC01
C:40-508
2c
2oncA01
A:40-508
2d
2oncB01
B:36-508
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Peptidase_S9_2oncD01 (D:559-765)
1b: PFAM_Peptidase_S9_2oncD02 (D:559-765)
1c: PFAM_Peptidase_S9_2oncD03 (D:559-765)
1d: PFAM_Peptidase_S9_2oncD04 (D:559-765)
2a: PFAM_DPPIV_N_2oncD05 (D:108-479)
2b: PFAM_DPPIV_N_2oncD06 (D:108-479)
2c: PFAM_DPPIV_N_2oncD07 (D:108-479)
2d: PFAM_DPPIV_N_2oncD08 (D:108-479)
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Clans
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)
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)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
AB_hydrolase
(347)
Family
:
Peptidase_S9
(57)
Homo sapiens (Human)
(33)
1a
Peptidase_S9-2oncD01
D:559-765
1b
Peptidase_S9-2oncD02
D:559-765
1c
Peptidase_S9-2oncD03
D:559-765
1d
Peptidase_S9-2oncD04
D:559-765
Clan
:
Beta_propeller
(192)
Family
:
DPPIV_N
(38)
Homo sapiens (Human)
(33)
2a
DPPIV_N-2oncD05
D:108-479
2b
DPPIV_N-2oncD06
D:108-479
2c
DPPIV_N-2oncD07
D:108-479
2d
DPPIV_N-2oncD08
D:108-479
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Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (510 KB)
Header - Asym.Unit
Biol.Unit 1 (257 KB)
Header - Biol.Unit 1
Biol.Unit 2 (252 KB)
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Biol.Unit 3 (251 KB)
Header - Biol.Unit 3
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