1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Chung, W.J.
Heddi, B.
Tera, M.
Iida, K.
Nagasawa, K.
Phan, A.T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
C32 H34 N10 O8
686.675
(12S,27S)-12,27-bis(4-aminobutyl)-4,30-dimethyl-3,7,14,18,22,29-hexaoxa-11,26,31,32,33,34,35,36-octaazaheptacyclo[26.2. 1.1~2,5~.1~6,9~.1~13,16~.1~17,20~.1~21,24~]hexatriaconta-1(30),2(36),4,6(35),8,13(34),15,17(33),19,21(32),23,28(31)-dode caene-10,25-dione
Telomestatin derivative
non-polymer
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
135
13495
13501
10.1021/ja405843r
23909929
Solution structure of an intramolecular (3 + 1) human telomeric g-quadruplex bound to a telomestatin derivative.
2013
10.2210/pdb2mb3/pdb
pdb_00002mb3
7591.883
DNA_(5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3')
1
syn
polymer
686.675
(12S,27S)-12,27-bis(4-aminobutyl)-4,30-dimethyl-3,7,14,18,22,29-hexaoxa-11,26,31,32,33,34,35,36-octaazaheptacyclo[26.2. 1.1~2,5~.1~6,9~.1~13,16~.1~17,20~.1~21,24~]hexatriaconta-1(30),2(36),4,6(35),8,13(34),15,17(33),19,21(32),23,28(31)-dode caene-10,25-dione
1
syn
non-polymer
no
no
(DT)(DT)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)
(DG)(DG)(DG)(DA)
TTGGGTTAGGGTTAGGGTTAGGGA
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
chem_comp
database_2
entity
pdbx_database_status
pdbx_entity_nonpoly
pdbx_nmr_software
struct_site
repository
Initial release
Database references
Data collection
Database references
Derived calculations
Other
Structure summary
1
0
2013-08-28
1
1
2013-09-25
1
2
2023-06-14
_chem_comp.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_entity.pdbx_description
_pdbx_database_status.status_code_nmr_data
_pdbx_entity_nonpoly.name
_pdbx_nmr_software.name
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BMRB
Y
RCSB
2013-07-24
REL
REL
REL
REL
L2H
(12S,27S)-12,27-bis(4-aminobutyl)-4,30-dimethyl-3,7,14,18,22,29-hexaoxa-11,26,31,32,33,34,35,36-octaazaheptacyclo[26.2. 1.1~2,5~.1~6,9~.1~13,16~.1~17,20~.1~21,24~]hexatriaconta-1(30),2(36),4,6(35),8,13(34),15,17(33),19,21(32),23,28(31)-dode caene-10,25-dione
579
279
structures with the lowest energy
100
10
2D 1H-1H TOCSY
2D 1H-1H TOCSY
2D 1H-1H NOESY
2D 1H-1H NOESY
2D 1H-1H NOESY
2D 1H-1H NOESY
2D 1H-13C HSQC aromatic
2D 1H-13C HSQC aromatic
2D 1H-13C HSQC aliphatic
2D 1H-13C HSQC aliphatic
2D 1H-13C HSQC aliphatic
2D 1H-13C HSQC aromatic
1D JRHMBC
2D 1H-31P HSQC
0.2-2
mM
0.2-2
mM
0.2-2
mM
0.2-2
mM
0.2
mM
[U-99% 13C; U-99% 15N]
0.2
mM
0.2
mM
[U-99% 13C; U-99% 15N]
0.2
mM
0.2-1
mM
[U-4% 13C]
0.2-1
mM
90
7
ambient
atm
310
K
90
7
298
K
40
7
298
K
DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics
1
lowest energy
0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H, 90% H2O/10% D2O
90% H2O/10% D2O
0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H, 100% D2O
100% D2O
0.2 mM [U-99% 13C; U-99% 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 mM L2H, 90% H2O/10% D2O
90% H2O/10% D2O
0.2 mM [U-99% 13C; U-99% 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 mM L2H, 100% D2O
100% D2O
0.2-1 mM [U-4% 13C] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-1 mM L2H, 90% H2O/10% D2O
90% H2O/10% D2O
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollman
refinement
Amber
Goddard
data analysis
Sparky
Goddard
chemical shift assignment
Sparky
Goddard
peak picking
Sparky
Schwieters, Kuszewski, Tjandra and Clore
refinement
X-PLOR NIH
Schwieters, Kuszewski, Tjandra and Clore
structure solution
X-PLOR NIH
Bruker Biospin
collection
TopSpin
600
Bruker
AMX
Bruker AMX
700
Bruker
AMX
Bruker AMX
400
Bruker
AMX
Bruker AMX
L2H
25
2
L2H
L2H
25
A
DT
1
n
1
DT
1
A
DT
2
n
2
DT
2
A
DG
3
n
3
DG
3
A
DG
4
n
4
DG
4
A
DG
5
n
5
DG
5
A
DT
6
n
6
DT
6
A
DT
7
n
7
DT
7
A
DA
8
n
8
DA
8
A
DG
9
n
9
DG
9
A
DG
10
n
10
DG
10
A
DG
11
n
11
DG
11
A
DT
12
n
12
DT
12
A
DT
13
n
13
DT
13
A
DA
14
n
14
DA
14
A
DG
15
n
15
DG
15
A
DG
16
n
16
DG
16
A
DG
17
n
17
DG
17
A
DT
18
n
18
DT
18
A
DT
19
n
19
DT
19
A
DA
20
n
20
DA
20
A
DG
21
n
21
DG
21
A
DG
22
n
22
DG
22
A
DG
23
n
23
DG
23
A
DA
24
n
24
DA
24
A
author_defined_assembly
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
A
HO5'
OP1
DT
DT
1
2
1.54
1
-3.61
0.60
122.90
119.29
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
1
-3.63
0.60
122.90
119.27
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
2
-3.83
0.60
122.90
119.07
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
3
-3.69
0.60
122.90
119.21
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
4
-3.64
0.60
122.90
119.26
A
A
A
C6
C5
C7
DT
DT
DT
1
1
1
N
6
-3.63
0.60
122.90
119.27
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
8
-3.73
0.60
122.90
119.17
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
9
-3.66
0.60
122.90
119.24
A
A
A
C6
C5
C7
DT
DT
DT
1
1
1
N
10
-3.71
0.60
122.90
119.19
A
A
A
C6
C5
C7
DT
DT
DT
6
6
6
N
10
-3.64
0.60
122.90
119.26
A
A
A
C6
C5
C7
DT
DT
DT
18
18
18
N
lowest energy, model1
Solution structure of an intramolecular (3+1) human telomeric G-quadruplex bound to a telomestatin derivative
1
N
N
2
N
N
hydrog
TYPE_6_PAIR
A
DG
3
A
N7
DG
3
1_555
A
DG
9
A
N2
DG
9
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
O6
DG
3
1_555
A
DG
9
A
N1
DG
9
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
N1
DG
3
1_555
A
DG
21
A
O6
DG
21
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
N2
DG
3
1_555
A
DG
21
A
N7
DG
21
1_555
hydrog
TYPE_6_PAIR
A
DG
4
A
N1
DG
4
1_555
A
DG
10
A
O6
DG
10
1_555
hydrog
TYPE_6_PAIR
A
DG
4
A
N2
DG
4
1_555
A
DG
10
A
N7
DG
10
1_555
hydrog
TYPE_6_PAIR
A
DG
4
A
N7
DG
4
1_555
A
DG
22
A
N2
DG
22
1_555
hydrog
TYPE_6_PAIR
A
DG
4
A
O6
DG
4
1_555
A
DG
22
A
N1
DG
22
1_555
hydrog
TYPE_6_PAIR
A
DG
5
A
N1
DG
5
1_555
A
DG
11
A
O6
DG
11
1_555
hydrog
TYPE_6_PAIR
A
DG
5
A
N2
DG
5
1_555
A
DG
11
A
N7
DG
11
1_555
hydrog
TYPE_27_PAIR
A
DG
5
A
N1
DG
5
1_555
A
DT
13
A
O4
DT
13
1_555
hydrog
TYPE_27_PAIR
A
DG
5
A
O6
DG
5
1_555
A
DT
13
A
N3
DT
13
1_555
hydrog
TYPE_6_PAIR
A
DG
5
A
N7
DG
5
1_555
A
DG
23
A
N2
DG
23
1_555
hydrog
TYPE_6_PAIR
A
DG
5
A
O6
DG
5
1_555
A
DG
23
A
N1
DG
23
1_555
hydrog
TYPE_6_PAIR
A
DG
9
A
N7
DG
9
1_555
A
DG
17
A
N2
DG
17
1_555
hydrog
TYPE_6_PAIR
A
DG
9
A
O6
DG
9
1_555
A
DG
17
A
N1
DG
17
1_555
hydrog
TYPE_6_PAIR
A
DG
10
A
N1
DG
10
1_555
A
DG
16
A
O6
DG
16
1_555
hydrog
TYPE_6_PAIR
A
DG
10
A
N2
DG
10
1_555
A
DG
16
A
N7
DG
16
1_555
hydrog
TYPE_6_PAIR
A
DG
11
A
N1
DG
11
1_555
A
DG
15
A
O6
DG
15
1_555
hydrog
TYPE_6_PAIR
A
DG
11
A
N2
DG
11
1_555
A
DG
15
A
N7
DG
15
1_555
hydrog
DT-DG MISPAIR
A
DT
13
A
O2
DT
13
1_555
A
DG
15
A
N1
DG
15
1_555
hydrog
REVERSED WATSON-CRICK
A
DT
13
A
N3
DT
13
1_555
A
DA
24
A
N1
DA
24
1_555
hydrog
REVERSED WATSON-CRICK
A
DT
13
A
O2
DT
13
1_555
A
DA
24
A
N6
DA
24
1_555
hydrog
TYPE_6_PAIR
A
DG
15
A
N1
DG
15
1_555
A
DG
23
A
O6
DG
23
1_555
hydrog
TYPE_6_PAIR
A
DG
15
A
N2
DG
15
1_555
A
DG
23
A
N7
DG
23
1_555
hydrog
TYPE_6_PAIR
A
DG
16
A
N1
DG
16
1_555
A
DG
22
A
O6
DG
22
1_555
hydrog
TYPE_6_PAIR
A
DG
16
A
N2
DG
16
1_555
A
DG
22
A
N7
DG
22
1_555
hydrog
TYPE_6_PAIR
A
DG
17
A
N7
DG
17
1_555
A
DG
21
A
N2
DG
21
1_555
hydrog
TYPE_6_PAIR
A
DG
17
A
O6
DG
17
1_555
A
DG
21
A
N1
DG
21
1_555
DNA/DNA INHIBITOR
intramolecular G-quadruplex, human telomere, anticancer targets, macrocyclic hexaoxazole, telomestatin derivative, DNA-DNA INHIBITOR complex
2MB3
PDB
1
2MB3
TTGGGTTAGGGTTAGGGTTAGGGA
1
24
2MB3
1
24
2MB3
A
1
1
24
BINDING SITE FOR RESIDUE L2H A 25
A
L2H
25
Software
9
A
DT
2
A
DT
2
9
1_555
A
DG
3
A
DG
3
9
1_555
A
DA
8
A
DA
8
9
1_555
A
DG
9
A
DG
9
9
1_555
A
DG
17
A
DG
17
9
1_555
A
DT
18
A
DT
18
9
1_555
A
DT
19
A
DT
19
9
1_555
A
DA
20
A
DA
20
9
1_555
A
DG
21
A
DG
21
9
1_555