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3CCB
Biol. Unit 1
Info
Asym.Unit (503 KB)
Biol.Unit 1 (253 KB)
Biol.Unit 2 (249 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN DPP4 IN COMPLEX WITH A BENZIMIDAZOLE DERIVATIVE
Authors
:
M. B. Wallace, R. J. Skene
Date
:
25 Feb 08 (Deposition) - 21 Oct 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.49
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Structure-Based Design, Denzimidazole Derivatives, Peptidase, Aminopeptidase, Glycoprotein, Hydrolase, Membrane, Protease, Secreted, Serine Protease, Signal-Anchor, Transmembrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. B. Wallace, J. Feng, Z. Zhang, R. J. Skene, L. Shi, C. L. Caster, D. B. Kassel, R. Xu, S. L. Gwaltney
Structure-Based Design And Synthesis Of Benzimidazole Derivatives As Dipeptidyl Peptidase Iv Inhibitors.
Bioorg. Med. Chem. Lett. V. 18 2362 2008
[
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Hetero Components
(2, 16)
Info
All Hetero Components
1a: 1-BIPHENYL-2-YLMETHANAMINE (B2Ya)
1b: 1-BIPHENYL-2-YLMETHANAMINE (B2Yb)
1c: 1-BIPHENYL-2-YLMETHANAMINE (B2Yc)
1d: 1-BIPHENYL-2-YLMETHANAMINE (B2Yd)
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)
2u: N-ACETYL-D-GLUCOSAMINE (NAGu)
2v: N-ACETYL-D-GLUCOSAMINE (NAGv)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
B2Y
2
Ligand/Ion
1-BIPHENYL-2-YLMETHANAMINE
2
NAG
14
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: BC9 (SOFTWARE)
13: CC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:85 , SER A:87
BINDING SITE FOR RESIDUE NAG A 801
02
AC2
SOFTWARE
ILE A:148 , ASN A:150
BINDING SITE FOR RESIDUE NAG A 802
03
AC3
SOFTWARE
ASN A:219 , THR A:221 , GLN A:308 , GLU A:309
BINDING SITE FOR RESIDUE NAG A 803
04
AC4
SOFTWARE
ILE A:194 , ASN A:229 , THR A:231 , GLU A:232
BINDING SITE FOR RESIDUE NAG A 804
05
AC5
SOFTWARE
TRP A:187 , ASN A:281
BINDING SITE FOR RESIDUE NAG A 806
06
AC6
SOFTWARE
TRP A:187
BINDING SITE FOR RESIDUE NAG A 807
07
AC7
SOFTWARE
ILE A:319 , ASN A:321 , SER A:349
BINDING SITE FOR RESIDUE NAG A 808
08
AC8
SOFTWARE
ARG B:147 , ILE B:148 , ASN B:150
BINDING SITE FOR RESIDUE NAG B 802
09
AC9
SOFTWARE
ASN B:219 , THR B:221 , GLN B:308 , GLU B:309
BINDING SITE FOR RESIDUE NAG B 803
10
BC1
SOFTWARE
ILE B:194 , ASN B:229 , THR B:231
BINDING SITE FOR RESIDUE NAG B 804
11
BC2
SOFTWARE
GLU B:232
BINDING SITE FOR RESIDUE NAG B 805
12
BC9
SOFTWARE
ARG A:125 , GLU A:205 , GLU A:206 , TYR A:547 , SER A:630 , TYR A:662
BINDING SITE FOR RESIDUE B2Y A 800
13
CC1
SOFTWARE
ARG B:125 , GLU B:205 , GLU B:206 , TYR B:547 , SER B:630 , TYR B:662 , TYR B:666 , HIS B:740
BINDING SITE FOR RESIDUE B2Y B 800
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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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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
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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_d3ccba1 (A:41-508)
1b: SCOP_d3ccbb1 (B:36-508)
1c: SCOP_d3ccbc1 (C:41-508)
1d: SCOP_d3ccbd1 (D:41-508)
2a: SCOP_d3ccba2 (A:509-766)
2b: SCOP_d3ccbb2 (B:509-766)
2c: SCOP_d3ccbc2 (C:509-766)
2d: SCOP_d3ccbd2 (D:509-766)
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Protein Domains
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)
(
)
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
d3ccba1
A:41-508
1b
d3ccbb1
B:36-508
1c
d3ccbc1
C:41-508
1d
d3ccbd1
D:41-508
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
alpha/beta-Hydrolases
(971)
Superfamily
:
alpha/beta-Hydrolases
(971)
Family
:
DPP6 catalytic domain-like
(63)
Protein domain
:
Dipeptidyl peptidase IV/CD26, C-terminal domain
(62)
Human (Homo sapiens) [TaxId: 9606]
(54)
2a
d3ccba2
A:509-766
2b
d3ccbb2
B:509-766
2c
d3ccbc2
C:509-766
2d
d3ccbd2
D:509-766
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_3ccbA02 (A:509-766)
1b: CATH_3ccbB02 (B:509-766)
1c: CATH_3ccbC02 (C:509-766)
1d: CATH_3ccbD02 (D:509-766)
2a: CATH_3ccbA01 (A:41-508)
2b: CATH_3ccbC01 (C:41-508)
2c: CATH_3ccbD01 (D:41-508)
2d: CATH_3ccbB01 (B:36-508)
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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
3ccbA02
A:509-766
1b
3ccbB02
B:509-766
1c
3ccbC02
C:509-766
1d
3ccbD02
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
3ccbA01
A:41-508
2b
3ccbC01
C:41-508
2c
3ccbD01
D:41-508
2d
3ccbB01
B:36-508
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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Asym.Unit (503 KB)
Header - Asym.Unit
Biol.Unit 1 (253 KB)
Header - Biol.Unit 1
Biol.Unit 2 (249 KB)
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