1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Gallego, J.
Reid, B.R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-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
C31 H30 N4 O4 2
522.594
N,N'-(3,7-DIAZANONYLENE)-BIS-NAPHTHALIMIDE
LU-79553
non-polymer
US
Biochemistry
BICHAW
0033
0006-2960
38
15104
15115
10.1021/bi9915869
10563793
Solution structure and dynamics of a complex between DNA and the antitumor bisnaphthalimide LU-79553: intercalated ring flipping on the millisecond time scale.
1999
10.2210/pdb1cx3/pdb
pdb_00001cx3
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
DNA DOUBLE HELIX INTERCALATED BY LU-79553
1808.229
DNA (5'-D(*AP*TP*GP*CP*AP*T)-3')
2
syn
polymer
522.594
N,N'-(3,7-DIAZANONYLENE)-BIS-NAPHTHALIMIDE
1
syn
non-polymer
no
no
(DA)(DT)(DG)(DC)(DA)(DT)
ATGCAT
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
-8.694
1
20
A
1
B
6
0.501
A_DA1:DT6_B
1
-1.686
-0.341
0.186
-0.096
18.791
1
20
A
2
B
5
-2.135
A_DT2:DA5_B
2
2.043
0.311
-0.226
-0.026
-3.043
1
19
A
3
B
4
-2.533
A_DG3:DC4_B
3
-1.545
-0.831
-0.099
-0.256
4.452
1
19
A
4
B
3
-2.607
A_DC4:DG3_B
4
-3.155
0.526
-0.095
-0.127
-17.640
1
20
A
5
B
2
-0.966
A_DA5:DT2_B
5
0.425
-0.336
-0.217
-0.041
8.513
1
20
A
6
B
1
0.944
A_DT6:DA1_B
6
-3.512
0.330
0.155
-0.094
2.435
26.653
A
A
1
2
11.226
B
B
6
5
2.604
5.125
-0.174
-0.357
AA_DA1DT2:DA5DT6_BB
1
3.981
-8.720
25.865
-1.823
1.193
6.637
22.346
A
A
2
3
9.503
B
B
5
4
6.766
3.654
-0.461
-0.223
AA_DT2DG3:DC4DA5_BB
2
-3.203
8.331
21.817
-3.403
-1.289
2.967
39.642
A
A
3
4
0.426
B
B
4
3
2.969
0.289
-0.017
-0.273
AA_DG3DC4:DG3DC4_BB
3
0.087
-0.128
39.641
-0.434
0.034
6.662
22.861
A
A
4
5
9.253
B
B
3
2
6.785
3.644
0.511
-0.330
AA_DC4DA5:DT2DG3_BB
4
2.611
-6.630
22.423
-3.528
0.642
2.455
27.228
A
A
5
6
11.710
B
B
2
1
2.625
5.461
0.130
-0.400
AA_DA5DT6:DA1DT2_BB
5
-3.577
7.671
26.448
-1.929
-0.982
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1999-11-19
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
1999-08-27
REL
NF
N,N'-(3,7-DIAZANONYLENE)-BIS-NAPHTHALIMIDE
STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
20
15
COSY
NOESY
ROESY
TOCSY
HP-HETCOR
20 mM SODIUM PHOSPHATE
7.20
1
atm
275.00
K
DISTANCE GEOMETRY, MOLECULAR DYNAMICS
SODIUM PHOSPHATE, EDTA
ZHU AND REID
refinement
BIRDER
1995
structure solution
DGII
structure solution
Amber
structure solution
BIRDER
500
Bruker
DRX
750
Bruker
DMX
NF
1
2
NF
NF
7
A
A
1
n
1
DA
1
A
T
2
n
2
DT
2
A
G
3
n
3
DG
3
A
C
4
n
4
DC
4
A
A
5
n
5
DA
5
A
T
6
n
6
DT
6
A
A
1
n
1
DA
1
B
T
2
n
2
DT
2
B
G
3
n
3
DG
3
B
C
4
n
4
DC
4
B
A
5
n
5
DA
5
B
T
6
n
6
DT
6
B
author_defined_assembly
2
dimeric
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
DA
5
0.054
SIDE CHAIN
1
B
DA
5
0.053
SIDE CHAIN
2
B
DT
2
0.066
SIDE CHAIN
3
A
DA
5
0.051
SIDE CHAIN
3
B
DA
5
0.052
SIDE CHAIN
4
A
DA
5
0.052
SIDE CHAIN
4
B
DA
5
0.053
SIDE CHAIN
6
B
DA
5
0.052
SIDE CHAIN
8
B
DA
5
0.075
SIDE CHAIN
9
A
DA
5
0.053
SIDE CHAIN
13
A
DA
5
0.053
SIDE CHAIN
13
B
DA
5
0.053
SIDE CHAIN
14
A
DA
5
0.053
SIDE CHAIN
15
B
DA
5
0.074
SIDE CHAIN
1
2.66
0.30
108.30
110.96
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
1
-3.69
0.60
122.90
119.21
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
1
3.24
0.30
108.30
111.54
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
2.18
0.30
108.30
110.48
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
1
2.75
0.30
108.30
111.05
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
1
-3.77
0.60
122.90
119.13
B
B
B
C6
C5
C7
DT
DT
DT
2
2
2
N
1
2.99
0.30
108.30
111.29
B
B
B
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
2.14
0.30
108.30
110.44
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
2
2.76
0.30
108.30
111.06
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
2
-3.75
0.60
122.90
119.15
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
2
3.02
0.30
108.30
111.32
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
2
1.92
0.30
108.30
110.22
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
2
2.82
0.30
108.30
111.12
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
2
3.99
0.30
108.30
112.29
B
B
B
O4'
C1'
N1
DT
DT
DT
2
2
2
N
2
7.41
1.20
119.70
127.11
B
B
B
C3'
O3'
P
DT
DT
DG
2
2
3
Y
2
2.67
0.30
108.30
110.97
B
B
B
O4'
C1'
N9
DA
DA
DA
5
5
5
N
2
1.92
0.30
108.30
110.22
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
3
2.72
0.30
108.30
111.02
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
3
2.86
0.30
108.30
111.16
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
3
1.96
0.30
108.30
110.26
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
3
2.67
0.30
108.30
110.97
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
3
-3.76
0.60
122.90
119.14
B
B
B
C6
C5
C7
DT
DT
DT
2
2
2
N
3
2.94
0.30
108.30
111.24
B
B
B
O4'
C1'
N9
DA
DA
DA
5
5
5
N
3
2.03
0.30
108.30
110.33
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
4
2.66
0.30
108.30
110.96
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
4
-3.77
0.60
122.90
119.13
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
4
3.37
0.30
108.30
111.67
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
4
2.09
0.30
108.30
110.39
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
4
2.84
0.30
108.30
111.14
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
4
-3.70
0.60
122.90
119.20
B
B
B
C6
C5
C7
DT
DT
DT
2
2
2
N
4
2.96
0.30
108.30
111.26
B
B
B
O4'
C1'
N9
DA
DA
DA
5
5
5
N
4
2.17
0.30
108.30
110.47
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
5
2.55
0.30
108.30
110.85
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
5
-3.65
0.60
122.90
119.25
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
5
2.97
0.30
108.30
111.27
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
5
1.97
0.30
108.30
110.27
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
5
2.52
0.30
108.30
110.82
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
5
3.92
0.30
108.30
112.22
B
B
B
O4'
C1'
N9
DA
DA
DA
5
5
5
N
5
1.87
0.30
108.30
110.17
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
6
2.62
0.30
108.30
110.92
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
6
2.87
0.30
108.30
111.17
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
6
1.91
0.30
108.30
110.21
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
6
2.71
0.30
108.30
111.01
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
6
-3.81
0.60
122.90
119.09
B
B
B
C6
C5
C7
DT
DT
DT
2
2
2
N
6
2.91
0.30
108.30
111.21
B
B
B
O4'
C1'
N9
DA
DA
DA
5
5
5
N
6
1.97
0.30
108.30
110.27
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
7
2.75
0.30
108.30
111.05
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
7
-3.65
0.60
122.90
119.25
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
7
2.93
0.30
108.30
111.23
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
7
1.90
0.30
108.30
110.20
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
7
2.79
0.30
108.30
111.09
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
7
-3.61
0.60
122.90
119.29
B
B
B
C6
C5
C7
DT
DT
DT
2
2
2
N
7
2.93
0.30
108.30
111.23
B
B
B
O4'
C1'
N9
DA
DA
DA
5
5
5
N
7
1.91
0.30
108.30
110.21
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
8
2.49
0.30
108.30
110.79
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
8
-3.64
0.60
122.90
119.26
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
8
4.34
0.30
108.30
112.64
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
8
2.07
0.30
108.30
110.37
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
8
2.63
0.30
108.30
110.93
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
8
-3.70
0.60
122.90
119.20
B
B
B
C6
C5
C7
DT
DT
DT
2
2
2
N
8
2.43
0.30
108.30
110.73
B
B
B
O4'
C1'
N1
DC
DC
DC
4
4
4
N
8
7.68
1.20
119.70
127.38
B
B
B
C3'
O3'
P
DC
DC
DA
4
4
5
Y
8
3.83
0.30
108.30
112.13
B
B
B
O4'
C1'
N9
DA
DA
DA
5
5
5
N
8
2.22
0.30
108.30
110.52
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
9
2.51
0.30
108.30
110.81
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
9
3.10
0.30
108.30
111.40
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
9
2.08
0.30
108.30
110.38
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
9
2.69
0.30
108.30
110.99
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
9
-3.71
0.60
122.90
119.19
B
B
B
C6
C5
C7
DT
DT
DT
2
2
2
N
9
2.79
0.30
108.30
111.09
B
B
B
O4'
C1'
N9
DA
DA
DA
5
5
5
N
9
1.87
0.30
108.30
110.17
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
10
2.73
0.30
108.30
111.03
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
10
-3.77
0.60
122.90
119.13
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
10
3.01
0.30
108.30
111.31
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
10
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
10
2.66
0.30
108.30
110.96
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
10
-3.65
0.60
122.90
119.25
B
B
B
C6
C5
C7
DT
DT
DT
2
2
2
N
10
3.31
0.30
108.30
111.61
B
B
B
O4'
C1'
N9
DA
DA
DA
5
5
5
N
10
2.13
0.30
108.30
110.43
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
11
2.76
0.30
108.30
111.06
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
11
3.01
0.30
108.30
111.31
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
11
1.99
0.30
108.30
110.29
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
11
2.81
0.30
108.30
111.11
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
11
-3.65
0.60
122.90
119.25
B
B
B
C6
C5
C7
DT
DT
DT
2
2
2
N
11
2.98
0.30
108.30
111.28
B
B
B
O4'
C1'
N9
DA
DA
DA
5
5
5
N
11
1.97
0.30
108.30
110.27
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
12
3.11
0.30
108.30
111.41
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
12
-3.74
0.60
122.90
119.16
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
12
1.86
0.30
108.30
110.16
A
A
A
O4'
C1'
N9
DG
DG
DG
3
3
3
N
12
2.73
0.30
108.30
111.03
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
12
1.91
0.30
108.30
110.21
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
12
2.83
0.30
108.30
111.13
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
12
-3.71
0.60
122.90
119.19
B
B
B
C6
C5
C7
DT
DT
DT
2
2
2
N
12
3.67
0.30
108.30
111.97
B
B
B
O4'
C1'
N9
DA
DA
DA
5
5
5
N
12
2.21
0.30
108.30
110.51
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
13
2.80
0.30
108.30
111.10
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
13
-3.77
0.60
122.90
119.13
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
13
3.01
0.30
108.30
111.31
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
13
2.16
0.30
108.30
110.46
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
13
2.67
0.30
108.30
110.97
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
13
-3.69
0.60
122.90
119.21
B
B
B
C6
C5
C7
DT
DT
DT
2
2
2
N
13
3.32
0.30
108.30
111.62
B
B
B
O4'
C1'
N9
DA
DA
DA
5
5
5
N
13
2.14
0.30
108.30
110.44
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
14
2.68
0.30
108.30
110.98
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
14
-3.65
0.60
122.90
119.25
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
14
3.36
0.30
108.30
111.66
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
14
2.13
0.30
108.30
110.43
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
14
2.70
0.30
108.30
111.00
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
14
-3.76
0.60
122.90
119.14
B
B
B
C6
C5
C7
DT
DT
DT
2
2
2
N
14
2.99
0.30
108.30
111.29
B
B
B
O4'
C1'
N9
DA
DA
DA
5
5
5
N
14
2.17
0.30
108.30
110.47
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
15
2.72
0.30
108.30
111.02
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
15
-3.78
0.60
122.90
119.12
A
A
A
C6
C5
C7
DT
DT
DT
2
2
2
N
15
2.87
0.30
108.30
111.17
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
15
1.99
0.30
108.30
110.29
A
A
A
O4'
C1'
N1
DT
DT
DT
6
6
6
N
15
2.84
0.30
108.30
111.14
B
B
B
O4'
C1'
N9
DA
DA
DA
1
1
1
N
15
7.62
1.20
119.70
127.32
B
B
B
C3'
O3'
P
DC
DC
DA
4
4
5
Y
15
3.77
0.30
108.30
112.07
B
B
B
O4'
C1'
N9
DA
DA
DA
5
5
5
N
15
2.22
0.30
108.30
110.52
B
B
B
O4'
C1'
N1
DT
DT
DT
6
6
6
N
SOLUTION STRUCTURE OF A COMPLEX BETWEEN D(ATGCAT)2 AND THE ANTITUMOR BISNAPHTHALIMIDE LU-79553
1
N
N
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
DA
1
A
N1
DA
1
1_555
B
DT
6
B
N3
DT
6
1_555
hydrog
WATSON-CRICK
A
DA
1
A
N6
DA
1
1_555
B
DT
6
B
O4
DT
6
1_555
hydrog
WATSON-CRICK
A
DT
2
A
N3
DT
2
1_555
B
DA
5
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
2
A
O4
DT
2
1_555
B
DA
5
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
B
DC
4
B
N3
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
DC
4
B
O2
DC
4
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
DC
4
B
N4
DC
4
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N3
DC
4
1_555
B
DG
3
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
4
A
N4
DC
4
1_555
B
DG
3
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
4
A
O2
DC
4
1_555
B
DG
3
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
2
B
N3
DT
2
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
2
B
O4
DT
2
1_555
hydrog
WATSON-CRICK
A
DT
6
A
N3
DT
6
1_555
B
DA
1
B
N1
DA
1
1_555
hydrog
WATSON-CRICK
A
DT
6
A
O4
DT
6
1_555
B
DA
1
B
N6
DA
1
1_555
DNA
TOPOISOMERASE, ANTICANCER, DNA, NAPHTHALIMIDE, INTERCALATION, DEOXYRIBONUCLEIC ACID
1CX3
PDB
1
1CX3
1
6
1CX3
1
6
1CX3
A
1
1
6
1
6
1CX3
1
6
1CX3
B
1
1
6
BINDING SITE FOR RESIDUE NF A 7
A
NF
7
Software
8
A
DT
2
A
DT
2
8
1_555
A
DG
3
A
DG
3
8
1_555
A
DC
4
A
DC
4
8
1_555
A
DA
5
A
DA
5
8
1_555
B
DT
2
B
DT
2
8
1_555
B
DG
3
B
DG
3
8
1_555
B
DC
4
B
DC
4
8
1_555
B
DA
5
B
DA
5
8
1_555
1
P 1