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3CUV
Asym. Unit
Info
Asym.Unit (158 KB)
Biol.Unit 1 (152 KB)
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(1)
Title
:
TRACKING STRUCTURE ACTIVITY RELATIONSHIPS OF GLYCOGEN PHOSPHORYLASE INHIBITORS: SYNTHESIS, KINETIC AND CRYSTALLOGRAPHIC EVALUATION OF ANALOGUES OF N-(-D-GLUCOPYRANOSYL)-N'-OXAMIDES
Authors
:
C. Kyritsi, E. D. Chrysina, D. D. Leonidas, S. E. Zographos, N. G. Oikonomakos
Date
:
17 Apr 08 (Deposition) - 21 Apr 09 (Release) - 21 Apr 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.93
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Glycogen Phosphorylase, Structure, Catalytic Site, Rational Inhibitor Design, Acetylation, Allosteric Enzyme, Carbohydrate Metabolism, Glycogen Metabolism, Glycosyltransferase, Nucleotide-Binding, Phosphoprotein, Pyridoxal Phosphate, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Czifrak, C. Kyritsi, N. Felfoldi, T. Dosca, P. Gergely, E. D. Chrysina, A. Siafaka-Kapadai, D. D. Leonidas, S. E. Zographos, N. G. Oikonomakos
Tracking Structure Activity Relationships Of Glycogen Phosphorylase Inhibitors: Synthesis, Kinetic And Crystallographic Evaluation Of Analogues Of N-(-D-Glucopyranosyl)-N'-Oxamides
To Be Published
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 17)
Info
All Hetero Components
1a: N-[OXO(PYRIDIN-2-YLAMINO)ACETYL]-B... (475a)
2a: DIMETHYL SULFOXIDE (DMSa)
2b: DIMETHYL SULFOXIDE (DMSb)
2c: DIMETHYL SULFOXIDE (DMSc)
2d: DIMETHYL SULFOXIDE (DMSd)
2e: DIMETHYL SULFOXIDE (DMSe)
2f: DIMETHYL SULFOXIDE (DMSf)
2g: DIMETHYL SULFOXIDE (DMSg)
2h: DIMETHYL SULFOXIDE (DMSh)
2i: DIMETHYL SULFOXIDE (DMSi)
2j: DIMETHYL SULFOXIDE (DMSj)
2k: DIMETHYL SULFOXIDE (DMSk)
2l: DIMETHYL SULFOXIDE (DMSl)
2m: DIMETHYL SULFOXIDE (DMSm)
2n: DIMETHYL SULFOXIDE (DMSn)
2o: DIMETHYL SULFOXIDE (DMSo)
3a: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
475
1
Ligand/Ion
N-[OXO(PYRIDIN-2-YLAMINO)ACETYL]-BETA-D-GLUCOPYRANOSYLAMINE
2
DMS
15
Ligand/Ion
DIMETHYL SULFOXIDE
3
LLP
1
Mod. Amino Acid
2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
[
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Sites
(16, 16)
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)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:136 , ASN A:282 , ASP A:283 , ASN A:284 , PHE A:285 , HIS A:377 , THR A:378 , VAL A:455 , ASN A:484 , TYR A:573 , GLU A:672 , ALA A:673 , SER A:674 , GLY A:675 , HOH A:1042 , HOH A:1161 , HOH A:1401
BINDING SITE FOR RESIDUE 475 A 998
02
AC2
SOFTWARE
VAL A:40 , TRP A:67 , ILE A:68 , ARG A:193
BINDING SITE FOR RESIDUE DMS A 931
03
AC3
SOFTWARE
VAL A:221 , LYS A:294 , DMS A:972
BINDING SITE FOR RESIDUE DMS A 936
04
AC4
SOFTWARE
HIS A:201 , TRP A:215 , ARG A:351 , LEU A:356 , HOH A:1066
BINDING SITE FOR RESIDUE DMS A 937
05
AC5
SOFTWARE
ARG A:519 , GLU A:701 , GLU A:702 , ALA A:703 , HOH A:1148
BINDING SITE FOR RESIDUE DMS A 938
06
AC6
SOFTWARE
GLU A:706 , PHE A:708 , PHE A:709 , ARG A:786
BINDING SITE FOR RESIDUE DMS A 939
07
AC7
SOFTWARE
ARG A:66 , LEU A:102 , ARG A:234 , ASN A:236 , ARG A:833 , HOH A:1101
BINDING SITE FOR RESIDUE DMS A 940
08
AC8
SOFTWARE
TYR A:548 , GLU A:552 , TYR A:553 , ARG A:649 , HOH A:1291
BINDING SITE FOR RESIDUE DMS A 942
09
AC9
SOFTWARE
GLN A:264 , LEU A:267 , ASP A:268 , ASN A:270 , LEU A:271 , ASN A:274
BINDING SITE FOR RESIDUE DMS A 945
10
BC1
SOFTWARE
TYR A:553 , PHE A:644 , LEU A:645 , GLU A:646 , HOH A:1117
BINDING SITE FOR RESIDUE DMS A 946
11
BC2
SOFTWARE
HIS A:767 , HOH A:1064
BINDING SITE FOR RESIDUE DMS A 947
12
BC3
SOFTWARE
THR A:197 , HOH A:1814
BINDING SITE FOR RESIDUE DMS A 948
13
BC4
SOFTWARE
HIS A:443 , ILE A:467 , PHE A:468 , LYS A:469 , ASP A:470 , PHE A:471
BINDING SITE FOR RESIDUE DMS A 955
14
BC5
SOFTWARE
ARG A:33 , HOH A:1407
BINDING SITE FOR RESIDUE DMS A 956
15
BC6
SOFTWARE
GLN A:408 , LEU A:411 , ASN A:412 , ALA A:415 , ASN A:595
BINDING SITE FOR RESIDUE DMS A 958
16
BC7
SOFTWARE
LEU A:271 , ASN A:274 , DMS A:936 , HOH A:1508
BINDING SITE FOR RESIDUE DMS A 972
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PHOSPHORYLASE (A:672-684)
;
View:
Select:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PHOSPHORYLASE
PS00102
Phosphorylase pyridoxal-phosphate attachment site.
PYGM_RABIT
673-685
1
A:672-684
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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.
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3cuva_ (A:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
UDP-Glycosyltransferase/glycogen phosphorylase
(296)
Superfamily
:
UDP-Glycosyltransferase/glycogen phosphorylase
(296)
Family
:
Oligosaccharide phosphorylase
(199)
Protein domain
:
automated matches
(106)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(99)
1a
d3cuva_
A:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3cuvA02 (A:486-812)
1b: CATH_3cuvA01 (A:9-485,A:813-835)
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Organisms
(
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(
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Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Glycogen Phosphorylase B;
(202)
Rabbit (Oryctolagus cuniculus)
(113)
1a
3cuvA02
A:486-812
1b
3cuvA01
A:9-485,A:813-835
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Pfam Domains
(0, 0)
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Chain A
Asymmetric Unit 1
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Asym.Unit (158 KB)
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