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3F8S
Biol. Unit 2
Info
Asym.Unit (251 KB)
Biol.Unit 1 (123 KB)
Biol.Unit 2 (124 KB)
Biol.Unit 3 (242 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIPEPTIDYL PEPTIDASE IV IN COMPLEX WITH INHIBITOR
Authors
:
M. J. Ammirati, S. Liu, D. W. Piotrowski
Date
:
13 Nov 08 (Deposition) - 23 Jun 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.43
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (1x)
Keywords
:
Dipeptidyl Peptidase 4, Complex, Aminopeptidase, Glycoprotein, Hydrolase, Membrane, Protease, Secreted, Serine Protease, Signal- Anchor, Transmembrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. J. Ammirati, K. M. Andrews, D. D. Boyer, A. M. Brodeur, D. E. Danley, S. D. Doran, B. Hulin, S. Liu, R. K. Mcpherson, S. J. Orena, J. C. Parker, J. Polivkova, X. Qiu, C. B. Soglia, J. L. Treadway, M. A. Vanvolkenburg D. C. Wilder, D. W. Piotrowski
(3, 3-Difluoro-Pyrrolidin-1-Yl)-[(2S, 4S)-(4-(4-Pyrimidin-2- Yl-Piperazin-1-Yl)-Pyrrolidin-2-Yl]-Methanone: A Potent, Selective, Orally Active Dipeptidyl Peptidase Iv Inhibitor.
Bioorg. Med. Chem. Lett. V. 19 1991 2009
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Hetero Components
(2, 7)
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)
2a: 2-(4-{(3S,5S)-5-[(3,3-DIFLUOROPYRR... (PF2a)
2b: 2-(4-{(3S,5S)-5-[(3,3-DIFLUOROPYRR... (PF2b)
View:
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Label:
No.
Name
Count
Type
Full Name
1
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
PF2
1
Ligand/Ion
2-(4-{(3S,5S)-5-[(3,3-DIFLUOROPYRROLIDIN-1-YL)CARBONYL]PYRROLIDIN-3-YL}PIPERAZIN-1-YL)PYRIMIDINE
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Sites
(7, 7)
Info
All Sites
1: AC6 (SOFTWARE)
2: AC7 (SOFTWARE)
3: AC8 (SOFTWARE)
4: AC9 (SOFTWARE)
5: BC1 (SOFTWARE)
6: BC2 (SOFTWARE)
7: BC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC6
SOFTWARE
VAL B:78 , ASN B:85 , SER B:86 , SER B:87 , TYR B:386 , GLN B:388 , THR B:395 , NAG B:797
BINDING SITE FOR RESIDUE NAG B 794
2
AC7
SOFTWARE
LYS B:391 , NAG B:794
BINDING SITE FOR RESIDUE NAG B 797
3
AC8
SOFTWARE
ASN B:229 , THR B:231 , NAG B:798
BINDING SITE FOR RESIDUE NAG B 796
4
AC9
SOFTWARE
NAG B:796
BINDING SITE FOR RESIDUE NAG B 798
5
BC1
SOFTWARE
ASN B:219 , THR B:221
BINDING SITE FOR RESIDUE NAG B 799
6
BC2
SOFTWARE
ILE B:319 , ASN B:321 , MET B:348 , SER B:349 , THR B:350
BINDING SITE FOR RESIDUE NAG B 800
7
BC4
SOFTWARE
ARG B:125 , GLU B:205 , GLU B:206 , PHE B:357 , SER B:630 , TYR B:631 , VAL B:656 , TYR B:662 , TYR B:666 , ASN B:710
BINDING SITE FOR RESIDUE PF2 B 900
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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, 1)
Info
All PROSITE Patterns/Profiles
1: PRO_ENDOPEP_SER (B:605-635)
;
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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
1
-
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, 4)
Info
All SCOP Domains
1a: SCOP_d3f8sa1 (A:39-508)
1b: SCOP_d3f8sb1 (B:39-508)
2a: SCOP_d3f8sa2 (A:509-766)
2b: SCOP_d3f8sb2 (B:509-766)
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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
d3f8sa1
A:39-508
1b
d3f8sb1
B:39-508
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
d3f8sa2
A:509-766
2b
d3f8sb2
B:509-766
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3f8sA02 (A:509-766)
1b: CATH_3f8sB02 (B:509-766)
2a: CATH_3f8sA01 (A:39-508)
2b: CATH_3f8sB01 (B:39-508)
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Organisms
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)
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)
Homo sapiens. Organism_taxid: 9606.
(1)
1a
3f8sA02
A:509-766
1b
3f8sB02
B: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)
Homo sapiens. Organism_taxid: 9606.
(1)
2a
3f8sA01
A:39-508
2b
3f8sB01
B:39-508
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Pfam Domains
(0, 0)
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Chain B
Asymmetric Unit 1
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Asym.Unit (251 KB)
Header - Asym.Unit
Biol.Unit 1 (123 KB)
Header - Biol.Unit 1
Biol.Unit 2 (124 KB)
Header - Biol.Unit 2
Biol.Unit 3 (242 KB)
Header - Biol.Unit 3
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