0.040355
0.000000
0.000000
0.000000
0.024295
0.000000
0.000000
0.000000
0.015265
0.00000
0.00000
0.00000
Nunn, C.M.
Neidle, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
24.780
41.160
65.510
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
H2 O
18.015
WATER
non-polymer
C17 H20 N4 O2
312.366
1,3-BIS(AMIDINOPHENOXY)PROPANE
non-polymer
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
N
C
N
12
R
C
Y
13
N
N
Y
14
N
C
Y
15
N
N
Y
16
N
C
Y
17
N
C
N
18
N
N
Y
19
N
N
Y
20
N
C
Y
21
N
N
Y
22
N
C
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
O
N
38
N
P
N
39
N
O
N
40
N
O
N
41
N
O
N
42
N
C
N
43
R
C
N
44
N
O
N
45
S
C
N
46
N
O
N
47
N
C
N
48
R
C
N
49
N
N
N
50
N
C
N
51
N
O
N
52
N
N
N
53
N
C
N
54
N
N
N
55
N
C
N
56
N
C
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
O
N
72
N
P
N
73
N
O
N
74
N
O
N
75
N
O
N
76
N
C
N
77
R
C
N
78
N
O
N
79
S
C
N
80
N
O
N
81
N
C
N
82
R
C
Y
83
N
N
Y
84
N
C
Y
85
N
N
Y
86
N
C
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
N
N
92
N
N
Y
93
N
C
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
O
N
109
N
P
N
110
N
O
N
111
N
O
N
112
N
O
N
113
N
C
N
114
R
C
N
115
N
O
N
116
S
C
N
117
N
O
N
118
N
C
N
119
R
C
N
120
N
N
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
C
N
125
N
O
N
126
N
C
N
127
N
C
N
128
N
C
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
O
N
145
N
H
N
146
N
H
Y
147
N
C
Y
148
N
C
Y
149
N
C
Y
150
N
C
Y
151
N
C
Y
152
N
C
N
153
N
C
N
154
N
N
N
155
N
N
Y
156
N
C
Y
157
N
C
Y
158
N
C
Y
159
N
C
Y
160
N
C
Y
161
N
C
N
162
N
C
N
163
N
N
N
164
N
N
N
165
N
C
N
166
N
O
N
167
N
C
N
168
N
C
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
Y
24
N
sing
Y
25
N
sing
Y
26
N
doub
N
27
N
sing
Y
28
N
sing
Y
29
N
sing
Y
30
N
doub
N
31
N
sing
Y
32
N
doub
N
33
N
sing
N
34
N
sing
Y
35
N
sing
Y
36
N
doub
N
37
N
sing
Y
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
doub
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
doub
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
sing
N
102
N
sing
Y
103
N
doub
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
doub
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
doub
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
Y
152
N
doub
Y
153
N
sing
N
154
N
sing
Y
155
N
sing
N
156
N
sing
Y
157
N
doub
N
158
N
sing
Y
159
N
sing
N
160
N
sing
Y
161
N
doub
N
162
N
sing
N
163
N
sing
N
164
N
doub
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
Y
169
N
doub
Y
170
N
sing
N
171
N
sing
Y
172
N
sing
N
173
N
sing
Y
174
N
doub
N
175
N
sing
Y
176
N
sing
N
177
N
sing
Y
178
N
doub
N
179
N
sing
N
180
N
sing
N
181
N
doub
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
US
J.Med.Chem.
JMCMAR
0151
0022-2623
38
2317
2325
10.1021/jm00013a008
7608897
Sequence-dependent drug binding to the minor groove of DNA: crystal structure of the DNA dodecamer d(CGCAAATTTGCG)2 complexed with propamidine.
1995
10.2210/pdb102d/pdb
pdb_0000102d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
289.00
1
AREA DETECTOR
XENTRONICS
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
3662.404
DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')
2
syn
polymer
312.366
1,3-BIS(AMIDINOPHENOXY)PROPANE
1
syn
non-polymer
18.015
water
73
nat
water
no
no
(DC)(DG)(DC)(DA)(DA)(DA)(DT)(DT)(DT)(DG)(DC)(DG)
CGCAAATTTGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
2.28
46.06
VAPOR DIFFUSION, SITTING DROP
7.00
pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
277.00
WATER
1
MPD
1
MGCL2
1
NA CACODYLATE
1
WATER
2
MPD
2
2.206
1
19
A
1
B
24
-5.599
A_DC1:DG24_B
1
-9.356
-0.109
0.184
-0.160
4.541
1
19
A
2
B
23
-4.717
A_DG2:DC23_B
2
-8.708
0.019
0.545
-0.290
-5.131
1
19
A
3
B
22
0.629
A_DC3:DG22_B
3
-6.485
0.050
0.134
-0.045
15.404
1
20
A
4
B
21
-2.999
A_DA4:DT21_B
4
-10.654
0.259
-0.268
-0.094
4.838
1
20
A
5
B
20
-1.543
A_DA5:DT20_B
5
-15.845
0.133
-0.128
-0.044
2.228
1
20
A
6
B
19
-4.332
A_DA6:DT19_B
6
-19.128
0.142
0.329
-0.035
-0.167
1
20
A
7
B
18
0.450
A_DT7:DA18_B
7
-18.014
0.015
0.332
-0.031
-0.759
1
20
A
8
B
17
-4.420
A_DT8:DA17_B
8
-16.903
-0.258
-0.166
-0.238
-7.042
1
20
A
9
B
16
-7.743
A_DT9:DA16_B
9
-10.913
-0.357
-0.318
-0.029
7.644
1
19
A
10
B
15
-1.804
A_DG10:DC15_B
10
0.533
0.034
0.299
-0.152
4.338
1
19
A
11
B
14
-0.926
A_DC11:DG14_B
11
-20.209
0.199
0.475
-0.224
0.173
1
19
A
12
B
13
-4.458
A_DG12:DC13_B
12
9.345
-0.186
-0.161
-0.323
3.444
37.511
A
A
1
2
3.823
B
B
24
23
3.460
2.454
-0.082
-0.065
AA_DC1DG2:DC23DG24_BB
1
-3.208
4.997
37.301
-0.441
-0.317
3.667
39.581
A
A
2
3
-5.026
B
B
23
22
3.635
-3.387
0.725
0.275
AA_DG2DC3:DG22DC23_BB
2
6.171
-9.158
38.974
0.853
-0.257
3.053
30.319
A
A
3
4
11.242
B
B
22
21
3.023
5.842
-0.570
0.604
AA_DC3DA4:DT21DG22_BB
3
1.418
-2.727
29.731
0.051
1.358
3.564
34.799
A
A
4
5
2.571
B
B
21
20
3.564
1.537
-0.080
0.094
AA_DA4DA5:DT20DT21_BB
4
-1.824
3.053
34.720
-0.098
-0.169
3.196
41.819
A
A
5
6
2.902
B
B
20
19
3.235
2.069
0.142
-0.386
AA_DA5DA6:DT19DT20_BB
5
-2.940
4.124
41.671
-0.753
-0.503
3.388
27.451
A
A
6
7
0.161
B
B
19
18
3.393
0.076
0.154
-0.802
AA_DA6DT7:DA18DT19_BB
6
-0.492
1.036
27.447
-1.709
-0.451
3.169
37.587
A
A
7
8
2.311
B
B
18
17
3.217
1.487
-0.310
-0.090
AA_DT7DT8:DA17DA18_BB
7
3.613
-5.618
37.391
-0.329
0.941
3.452
39.009
A
A
8
9
-3.085
B
B
17
16
3.487
-2.059
-0.291
0.217
AA_DT8DT9:DA16DA17_BB
8
2.067
-3.099
38.904
0.588
0.701
2.882
34.516
A
A
9
10
-3.454
B
B
16
15
3.102
-2.038
0.645
0.990
AA_DT9DG10:DC15DA16_BB
9
-6.133
10.394
33.924
1.961
-1.964
3.468
38.501
A
A
10
11
-10.641
B
B
15
14
3.577
-6.980
-0.512
0.347
AA_DG10DC11:DG14DC15_BB
10
-0.564
0.860
37.883
1.467
0.701
3.567
39.173
A
A
11
12
-10.821
B
B
14
13
3.735
-7.186
0.328
0.643
AA_DC11DG12:DC13DG14_BB
11
6.467
-9.739
38.006
1.935
0.389
chem_comp_atom
chem_comp_bond
database_2
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
1995-02-07
1
1
2008-05-22
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BNL
Y
NDB
1994-12-15
REL
REL
TNT
1,3-BIS(AMIDINOPHENOXY)PROPANE
HOH
water
TNT
25
2
TNT
TNT
25
B
HOH
26
3
HOH
HOH
26
A
HOH
27
3
HOH
HOH
27
A
HOH
29
3
HOH
HOH
29
A
HOH
31
3
HOH
HOH
31
A
HOH
34
3
HOH
HOH
34
A
HOH
35
3
HOH
HOH
35
A
HOH
37
3
HOH
HOH
37
A
HOH
38
3
HOH
HOH
38
A
HOH
40
3
HOH
HOH
40
A
HOH
41
3
HOH
HOH
41
A
HOH
42
3
HOH
HOH
42
A
HOH
44
3
HOH
HOH
44
A
HOH
45
3
HOH
HOH
45
A
HOH
47
3
HOH
HOH
47
A
HOH
50
3
HOH
HOH
50
A
HOH
52
3
HOH
HOH
52
A
HOH
53
3
HOH
HOH
53
A
HOH
54
3
HOH
HOH
54
A
HOH
59
3
HOH
HOH
59
A
HOH
63
3
HOH
HOH
63
A
HOH
64
3
HOH
HOH
64
A
HOH
65
3
HOH
HOH
65
A
HOH
67
3
HOH
HOH
67
A
HOH
69
3
HOH
HOH
69
A
HOH
71
3
HOH
HOH
71
A
HOH
74
3
HOH
HOH
74
A
HOH
75
3
HOH
HOH
75
A
HOH
80
3
HOH
HOH
80
A
HOH
81
3
HOH
HOH
81
A
HOH
82
3
HOH
HOH
82
A
HOH
83
3
HOH
HOH
83
A
HOH
86
3
HOH
HOH
86
A
HOH
87
3
HOH
HOH
87
A
HOH
90
3
HOH
HOH
90
A
HOH
91
3
HOH
HOH
91
A
HOH
92
3
HOH
HOH
92
A
HOH
94
3
HOH
HOH
94
A
HOH
97
3
HOH
HOH
97
A
HOH
28
3
HOH
HOH
28
B
HOH
30
3
HOH
HOH
30
B
HOH
32
3
HOH
HOH
32
B
HOH
33
3
HOH
HOH
33
B
HOH
36
3
HOH
HOH
36
B
HOH
39
3
HOH
HOH
39
B
HOH
43
3
HOH
HOH
43
B
HOH
46
3
HOH
HOH
46
B
HOH
48
3
HOH
HOH
48
B
HOH
49
3
HOH
HOH
49
B
HOH
51
3
HOH
HOH
51
B
HOH
55
3
HOH
HOH
55
B
HOH
56
3
HOH
HOH
56
B
HOH
57
3
HOH
HOH
57
B
HOH
58
3
HOH
HOH
58
B
HOH
60
3
HOH
HOH
60
B
HOH
61
3
HOH
HOH
61
B
HOH
62
3
HOH
HOH
62
B
HOH
66
3
HOH
HOH
66
B
HOH
68
3
HOH
HOH
68
B
HOH
70
3
HOH
HOH
70
B
HOH
72
3
HOH
HOH
72
B
HOH
73
3
HOH
HOH
73
B
HOH
76
3
HOH
HOH
76
B
HOH
77
3
HOH
HOH
77
B
HOH
78
3
HOH
HOH
78
B
HOH
79
3
HOH
HOH
79
B
HOH
84
3
HOH
HOH
84
B
HOH
85
3
HOH
HOH
85
B
HOH
88
3
HOH
HOH
88
B
HOH
89
3
HOH
HOH
89
B
HOH
93
3
HOH
HOH
93
B
HOH
95
3
HOH
HOH
95
B
HOH
96
3
HOH
HOH
96
B
HOH
98
3
HOH
HOH
98
B
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
A
4
n
4
DA
4
A
A
5
n
5
DA
5
A
A
6
n
6
DA
6
A
T
7
n
7
DT
7
A
T
8
n
8
DT
8
A
T
9
n
9
DT
9
A
G
10
n
10
DG
10
A
C
11
n
11
DC
11
A
G
12
n
12
DG
12
A
C
13
n
1
DC
13
B
G
14
n
2
DG
14
B
C
15
n
3
DC
15
B
A
16
n
4
DA
16
B
A
17
n
5
DA
17
B
A
18
n
6
DA
18
B
T
19
n
7
DT
19
B
T
20
n
8
DT
20
B
T
21
n
9
DT
21
B
G
22
n
10
DG
22
B
C
23
n
11
DC
23
B
G
24
n
12
DG
24
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
5.10
0.60
118.90
124.00
A
A
A
N1
C2
O2
DC
DC
DC
1
1
1
N
1
8.02
1.20
119.70
127.72
A
A
A
C3'
O3'
P
DG
DG
DC
2
2
3
Y
1
5.31
0.70
110.30
115.61
A
A
A
C1'
O4'
C4'
DC
DC
DC
3
3
3
N
1
-6.42
0.80
105.90
99.48
A
A
A
O4'
C1'
C2'
DC
DC
DC
3
3
3
N
1
6.08
0.30
108.30
114.38
A
A
A
O4'
C1'
N1
DC
DC
DC
3
3
3
N
1
-2.69
0.40
121.90
119.21
A
A
A
N3
C4
C5
DC
DC
DC
3
3
3
N
1
5.94
0.60
118.90
124.84
A
A
A
N1
C2
O2
DC
DC
DC
3
3
3
N
1
-7.03
0.70
121.90
114.87
A
A
A
N3
C2
O2
DC
DC
DC
3
3
3
N
1
-12.53
1.90
104.00
91.47
A
A
A
O3'
P
O5'
DC
DA
DA
3
4
4
Y
1
5.87
0.70
110.30
116.17
A
A
A
C1'
O4'
C4'
DA
DA
DA
4
4
4
N
1
2.98
0.30
108.30
111.28
A
A
A
O4'
C1'
N9
DA
DA
DA
4
4
4
N
1
-2.68
0.40
105.80
103.12
A
A
A
C8
N9
C4
DA
DA
DA
4
4
4
N
1
4.25
0.70
110.30
114.55
A
A
A
C1'
O4'
C4'
DA
DA
DA
6
6
6
N
1
-5.21
0.80
105.90
100.69
A
A
A
O4'
C1'
C2'
DA
DA
DA
6
6
6
N
1
4.33
0.50
129.30
133.63
A
A
A
N1
C2
N3
DA
DA
DA
6
6
6
N
1
3.59
0.40
105.80
109.39
A
A
A
N9
C4
C5
DA
DA
DA
6
6
6
N
1
-5.42
0.80
105.90
100.48
A
A
A
O4'
C1'
C2'
DT
DT
DT
7
7
7
N
1
11.31
0.30
108.30
119.61
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
1
-5.55
0.60
122.30
116.75
A
A
A
N3
C2
O2
DT
DT
DT
7
7
7
N
1
4.82
0.60
118.00
122.82
A
A
A
C4
C5
C6
DT
DT
DT
8
8
8
N
1
-4.28
0.60
122.30
118.02
A
A
A
N3
C2
O2
DT
DT
DT
8
8
8
N
1
13.00
1.20
119.70
132.70
A
A
A
C3'
O3'
P
DT
DT
DT
8
8
9
Y
1
-10.16
1.60
120.90
110.74
A
A
A
P
O5'
C5'
DT
DT
DT
9
9
9
N
1
5.43
0.70
110.30
115.73
A
A
A
C1'
O4'
C4'
DT
DT
DT
9
9
9
N
1
-6.07
0.80
105.90
99.83
A
A
A
O4'
C1'
C2'
DT
DT
DT
9
9
9
N
1
3.88
0.60
114.60
118.48
A
A
A
N1
C2
N3
DT
DT
DT
9
9
9
N
1
-5.63
0.60
122.30
116.67
A
A
A
N3
C2
O2
DT
DT
DT
9
9
9
N
1
4.71
0.30
108.30
113.01
A
A
A
O4'
C1'
N9
DG
DG
DG
10
10
10
N
1
15.02
1.20
119.70
134.72
A
A
A
C3'
O3'
P
DG
DG
DC
10
10
11
Y
1
-2.53
0.40
121.90
119.37
A
A
A
N3
C4
C5
DC
DC
DC
11
11
11
N
1
7.79
1.10
109.80
117.59
A
A
A
C5'
C4'
O4'
DG
DG
DG
12
12
12
N
1
3.98
0.60
126.00
129.98
A
A
A
N3
C4
N9
DG
DG
DG
12
12
12
N
1
4.64
0.70
118.00
122.64
B
B
B
N3
C4
N4
DC
DC
DC
13
13
13
N
1
4.20
0.70
110.30
114.50
B
B
B
C1'
O4'
C4'
DG
DG
DG
14
14
14
N
1
-5.34
0.80
105.90
100.56
B
B
B
O4'
C1'
C2'
DG
DG
DG
14
14
14
N
1
6.84
0.30
108.30
115.14
B
B
B
O4'
C1'
N9
DG
DG
DG
14
14
14
N
1
4.28
0.70
110.30
114.58
B
B
B
C1'
O4'
C4'
DC
DC
DC
15
15
15
N
1
-5.82
0.80
105.90
100.08
B
B
B
O4'
C1'
C2'
DC
DC
DC
15
15
15
N
1
4.35
0.30
108.30
112.65
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
3.64
0.60
118.90
122.54
B
B
B
N1
C2
O2
DC
DC
DC
15
15
15
N
1
-3.91
0.50
129.30
125.39
B
B
B
N1
C2
N3
DA
DA
DA
16
16
16
N
1
4.85
0.50
110.60
115.45
B
B
B
C2
N3
C4
DA
DA
DA
16
16
16
N
1
4.76
0.70
110.30
115.06
B
B
B
C1'
O4'
C4'
DA
DA
DA
17
17
17
N
1
-4.92
0.80
105.90
100.98
B
B
B
O4'
C1'
C2'
DA
DA
DA
17
17
17
N
1
6.51
0.30
108.30
114.81
B
B
B
O4'
C1'
N9
DA
DA
DA
17
17
17
N
1
2.82
0.40
105.80
108.62
B
B
B
N9
C4
C5
DA
DA
DA
17
17
17
N
1
3.54
0.30
108.30
111.84
B
B
B
O4'
C1'
N9
DA
DA
DA
18
18
18
N
1
-9.72
1.60
120.90
111.18
B
B
B
P
O5'
C5'
DT
DT
DT
19
19
19
N
1
6.98
0.30
108.30
115.28
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
1
3.65
0.60
114.60
118.25
B
B
B
N1
C2
N3
DT
DT
DT
19
19
19
N
1
4.35
0.60
118.00
122.35
B
B
B
C4
C5
C6
DT
DT
DT
19
19
19
N
1
4.65
0.70
124.90
129.55
B
B
B
C5
C4
O4
DT
DT
DT
19
19
19
N
1
-4.17
0.60
122.90
118.73
B
B
B
C6
C5
C7
DT
DT
DT
19
19
19
N
1
4.43
0.60
114.60
119.03
B
B
B
N1
C2
N3
DT
DT
DT
21
21
21
N
1
3.96
0.60
118.00
121.96
B
B
B
C4
C5
C6
DT
DT
DT
21
21
21
N
1
-6.13
0.60
122.30
116.17
B
B
B
N3
C2
O2
DT
DT
DT
21
21
21
N
1
-3.04
0.40
104.50
101.46
B
B
B
O4'
C4'
C3'
DG
DG
DG
22
22
22
N
1
-5.63
0.80
102.40
96.77
B
B
B
C3'
C2'
C1'
DG
DG
DG
22
22
22
N
1
4.83
0.30
108.30
113.13
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
-3.71
0.50
128.60
124.89
B
B
B
N3
C4
C5
DG
DG
DG
22
22
22
N
1
9.25
0.30
108.30
117.55
B
B
B
O4'
C1'
N1
DC
DC
DC
23
23
23
N
1
4.11
0.60
118.90
123.01
B
B
B
N1
C2
O2
DC
DC
DC
23
23
23
N
1
5.97
0.70
118.00
123.97
B
B
B
N3
C4
N4
DC
DC
DC
23
23
23
N
1
-5.40
0.70
120.20
114.80
B
B
B
C5
C4
N4
DC
DC
DC
23
23
23
N
1
-11.25
1.80
114.10
102.85
B
B
B
C5'
C4'
C3'
DG
DG
DG
24
24
24
N
1
5.20
0.30
108.30
113.50
B
B
B
O4'
C1'
N9
DG
DG
DG
24
24
24
N
1
A
A
O3'
C3'
DT
DT
7
7
-0.036
0.006
1.419
1.383
N
1
A
A
C5
C7
DT
DT
7
7
0.048
0.006
1.496
1.544
N
1
B
B
O3'
C3'
DC
DC
13
13
-0.045
0.006
1.419
1.374
N
1
B
B
C3'
C2'
DG
DG
14
14
-0.048
0.008
1.516
1.468
N
1
B
B
C4'
C3'
DA
DA
17
17
-0.084
0.010
1.521
1.437
N
1
B
B
N9
C4
DA
DA
17
17
-0.036
0.006
1.374
1.338
N
1
B
B
C5'
C4'
DG
DG
22
22
0.059
0.007
1.512
1.571
N
0.1550000
0.1550000
2.200
8.000
842
90.800
1
2.000
TR
isotropic
TR
isotropic
2.200
8.000
73
582
23
486
0
0.022
4.00
fix
fix
2.200
102D
12110
3410
0.0530000
1
refinement
X-PLOR
data scaling
XENGEN
SEQUENCE-DEPENDENT DRUG BINDING TO THE MINOR GROOVE OF DNA: THE CRYSTAL STRUCTURE OF THE DNA DODECAMER D(CGCAAATTTGCG)2 COMPLEXED WITH PROPAMIDINE
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
hydrog
WATSON-CRICK
A
DC
1
A
N3
DC
1
1_555
B
DG
24
B
N1
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
N4
DC
1
1_555
B
DG
24
B
O6
DG
12
1_555
hydrog
WATSON-CRICK
A
DC
1
A
O2
DC
1
1_555
B
DG
24
B
N2
DG
12
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
DC
23
B
N3
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
DC
23
B
O2
DC
11
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
DC
23
B
N4
DC
11
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N3
DC
3
1_555
B
DG
22
B
N1
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
N4
DC
3
1_555
B
DG
22
B
O6
DG
10
1_555
hydrog
WATSON-CRICK
A
DC
3
A
O2
DC
3
1_555
B
DG
22
B
N2
DG
10
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N1
DA
4
1_555
B
DT
21
B
N3
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
4
A
N6
DA
4
1_555
B
DT
21
B
O4
DT
9
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
20
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
20
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
B
DT
19
B
N3
DT
7
1_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
B
DT
19
B
O4
DT
7
1_555
hydrog
WATSON-CRICK
A
DT
7
A
N3
DT
7
1_555
B
DA
18
B
N1
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
7
A
O4
DT
7
1_555
B
DA
18
B
N6
DA
6
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
17
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
17
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
9
A
N3
DT
9
1_555
B
DA
16
B
N1
DA
4
1_555
hydrog
WATSON-CRICK
A
DT
9
A
O4
DT
9
1_555
B
DA
16
B
N6
DA
4
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N1
DG
10
1_555
B
DC
15
B
N3
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
N2
DG
10
1_555
B
DC
15
B
O2
DC
3
1_555
hydrog
WATSON-CRICK
A
DG
10
A
O6
DG
10
1_555
B
DC
15
B
N4
DC
3
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N3
DC
11
1_555
B
DG
14
B
N1
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
N4
DC
11
1_555
B
DG
14
B
O6
DG
2
1_555
hydrog
WATSON-CRICK
A
DC
11
A
O2
DC
11
1_555
B
DG
14
B
N2
DG
2
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N1
DG
12
1_555
B
DC
13
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
N2
DG
12
1_555
B
DC
13
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
12
A
O6
DG
12
1_555
B
DC
13
B
N4
DC
1
1_555
DNA
B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DNA
102D
PDB
1
102D
1
12
102D
1
12
102D
A
1
1
12
13
24
102D
13
24
102D
B
1
1
12
BINDING SITE FOR RESIDUE TNT B 25
B
TNT
25
Software
11
A
DA
6
A
DA
6
11
1_555
A
DT
7
A
DT
7
11
1_555
A
DT
8
A
DT
8
11
1_555
A
DT
9
A
DT
9
11
1_555
A
DG
10
A
DG
10
11
1_555
B
DA
18
B
DA
6
11
1_555
B
DT
19
B
DT
7
11
1_555
B
DT
20
B
DT
8
11
1_555
B
DT
21
B
DT
9
11
1_555
B
HOH
32
E
HOH
11
1_555
B
HOH
36
E
HOH
11
1_555
19
P 21 21 21