0.040502
0.000000
0.000000
0.000000
0.024795
0.000000
0.000000
0.000000
0.015044
0.00000
0.00000
0.00000
Nunn, C.M.
Jenkins, T.C.
Neidle, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
24.690
40.330
66.470
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
C18 H22 N4 O3
342.392
1,5-DI(4-AMIDINOPHENOXY)-3-OXA-PENTANE
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
C
N
155
N
C
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
C
N
164
N
C
N
165
N
N
N
166
N
N
N
167
N
N
N
168
N
N
N
169
N
O
N
170
N
O
N
171
N
O
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
190
N
H
N
191
N
H
N
192
N
H
N
193
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
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
Y
173
N
doub
Y
174
N
sing
N
175
N
sing
Y
176
N
sing
N
177
N
sing
Y
178
N
doub
N
179
N
sing
Y
180
N
sing
N
181
N
sing
Y
182
N
doub
N
183
N
sing
N
184
N
sing
N
185
E
doub
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
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
IX
Eur.J.Biochem.
EJBCAI
0262
0014-2956
226
953
961
10.1111/j.1432-1033.1994.00953.x
7813486
Crystal structure of gamma-oxapentamidine complexed with d(CGCGAATTCGCG)2. The effects of drug structural change on DNA minor-groove recognition.
1994
10.2210/pdb166d/pdb
pdb_0000166d
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
287.00
1
AREA DETECTOR
XENTRONICS
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
3663.392
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
2
syn
polymer
342.392
1,5-DI(4-AMIDINOPHENOXY)-3-OXA-PENTANE
1
syn
non-polymer
18.015
water
73
nat
water
no
no
(DC)(DG)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG)
CGCGAATTCGCG
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
2.26
45.54
VAPOR DIFFUSION, SITTING DROP
7.00
pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 286.00K
286.00
WATER
1
MPD
1
MGCL2
1
NA CACODYLATE
1
WATER
2
MPD
2
8.950
1
19
A
1
B
24
-1.197
A_DC1:DG24_B
1
-11.784
0.115
-0.124
-0.107
-2.550
1
19
A
2
B
23
-6.523
A_DG2:DC23_B
2
-12.619
-0.322
0.227
-0.375
-3.915
1
19
A
3
B
22
1.618
A_DC3:DG22_B
3
-6.686
0.179
-0.009
-0.305
9.471
1
19
A
4
B
21
-0.747
A_DG4:DC21_B
4
-9.558
-0.126
0.169
-0.234
1.308
1
20
A
5
B
20
-0.088
A_DA5:DT20_B
5
-15.344
0.126
-0.277
-0.166
1.299
1
20
A
6
B
19
6.540
A_DA6:DT19_B
6
-18.727
0.140
0.062
-0.011
0.635
1
20
A
7
B
18
2.184
A_DT7:DA18_B
7
-18.515
0.033
0.161
-0.171
0.159
1
20
A
8
B
17
1.703
A_DT8:DA17_B
8
-14.541
-0.188
-0.065
-0.186
-5.886
1
19
A
9
B
16
-1.925
A_DC9:DG16_B
9
-14.246
-0.084
-0.075
-0.148
4.002
1
19
A
10
B
15
-2.868
A_DG10:DC15_B
10
-4.018
-0.102
0.362
-0.306
-1.689
1
19
A
11
B
14
-4.472
A_DC11:DG14_B
11
-19.804
0.112
0.696
-0.274
2.659
1
19
A
12
B
13
-8.169
A_DG12:DC13_B
12
12.535
-0.245
-0.077
-0.293
3.700
39.046
A
A
1
2
9.933
B
B
24
23
3.686
6.601
-0.439
0.236
AA_DC1DG2:DC23DG24_BB
1
-3.488
5.248
38.353
-0.554
0.177
3.437
38.818
A
A
2
3
-8.077
B
B
23
22
3.482
-5.348
0.695
0.414
AA_DG2DC3:DG22DC23_BB
2
2.875
-4.342
38.358
1.317
-0.673
3.206
28.471
A
A
3
4
18.026
B
B
22
21
3.085
8.728
-0.122
0.881
AA_DC3DG4:DC21DG22_BB
3
0.170
-0.351
27.126
-0.178
0.286
3.486
39.234
A
A
4
5
7.375
B
B
21
20
3.539
4.937
-0.255
-0.034
AA_DG4DA5:DT20DC21_BB
4
2.515
-3.758
38.856
-0.687
0.703
3.141
36.319
A
A
5
6
5.672
B
B
20
19
3.219
3.525
0.239
-0.285
AA_DA5DA6:DT19DT20_BB
5
-3.549
5.711
35.985
-0.938
-0.867
3.332
31.126
A
A
6
7
-4.869
B
B
19
18
3.299
-2.610
0.034
-0.538
AA_DA6DT7:DA18DT19_BB
6
0.129
-0.240
31.019
-0.497
-0.038
3.226
34.520
A
A
7
8
3.683
B
B
18
17
3.282
2.180
-0.144
-0.259
AA_DT7DT8:DA17DA18_BB
7
3.770
-6.369
34.252
-0.774
0.826
3.387
40.109
A
A
8
9
-1.280
B
B
17
16
3.392
-0.878
-0.131
0.236
AA_DT8DC9:DG16DA17_BB
8
-0.491
0.716
40.097
0.448
0.133
3.391
32.497
A
A
9
10
5.907
B
B
16
15
3.366
3.291
0.267
1.045
AA_DC9DG10:DC15DG16_BB
9
-4.253
7.633
32.061
1.269
-1.251
3.524
42.632
A
A
10
11
-17.585
B
B
15
14
3.636
-12.570
-1.331
0.389
AA_DG10DC11:DG14DC15_BB
10
-6.084
8.512
40.381
1.962
1.140
3.537
36.501
A
A
11
12
-14.429
B
B
14
13
3.507
-8.874
1.011
0.025
AA_DC11DG12:DC13DG14_BB
11
8.426
-13.700
34.454
1.403
-0.320
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
1994-10-15
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
1994-03-17
REL
REL
PET
1,5-DI(4-AMIDINOPHENOXY)-3-OXA-PENTANE
HOH
water
PET
25
2
PET
PET
25
B
HOH
26
3
HOH
HOH
26
A
HOH
27
3
HOH
HOH
27
A
HOH
30
3
HOH
HOH
30
A
HOH
40
3
HOH
HOH
40
A
HOH
43
3
HOH
HOH
43
A
HOH
44
3
HOH
HOH
44
A
HOH
46
3
HOH
HOH
46
A
HOH
47
3
HOH
HOH
47
A
HOH
49
3
HOH
HOH
49
A
HOH
50
3
HOH
HOH
50
A
HOH
51
3
HOH
HOH
51
A
HOH
52
3
HOH
HOH
52
A
HOH
56
3
HOH
HOH
56
A
HOH
57
3
HOH
HOH
57
A
HOH
59
3
HOH
HOH
59
A
HOH
61
3
HOH
HOH
61
A
HOH
62
3
HOH
HOH
62
A
HOH
68
3
HOH
HOH
68
A
HOH
74
3
HOH
HOH
74
A
HOH
78
3
HOH
HOH
78
A
HOH
79
3
HOH
HOH
79
A
HOH
83
3
HOH
HOH
83
A
HOH
85
3
HOH
HOH
85
A
HOH
86
3
HOH
HOH
86
A
HOH
87
3
HOH
HOH
87
A
HOH
88
3
HOH
HOH
88
A
HOH
90
3
HOH
HOH
90
A
HOH
91
3
HOH
HOH
91
A
HOH
92
3
HOH
HOH
92
A
HOH
93
3
HOH
HOH
93
A
HOH
97
3
HOH
HOH
97
A
HOH
98
3
HOH
HOH
98
A
HOH
28
3
HOH
HOH
28
B
HOH
29
3
HOH
HOH
29
B
HOH
31
3
HOH
HOH
31
B
HOH
32
3
HOH
HOH
32
B
HOH
33
3
HOH
HOH
33
B
HOH
34
3
HOH
HOH
34
B
HOH
35
3
HOH
HOH
35
B
HOH
36
3
HOH
HOH
36
B
HOH
37
3
HOH
HOH
37
B
HOH
38
3
HOH
HOH
38
B
HOH
39
3
HOH
HOH
39
B
HOH
41
3
HOH
HOH
41
B
HOH
42
3
HOH
HOH
42
B
HOH
45
3
HOH
HOH
45
B
HOH
48
3
HOH
HOH
48
B
HOH
53
3
HOH
HOH
53
B
HOH
54
3
HOH
HOH
54
B
HOH
55
3
HOH
HOH
55
B
HOH
58
3
HOH
HOH
58
B
HOH
60
3
HOH
HOH
60
B
HOH
63
3
HOH
HOH
63
B
HOH
64
3
HOH
HOH
64
B
HOH
65
3
HOH
HOH
65
B
HOH
66
3
HOH
HOH
66
B
HOH
67
3
HOH
HOH
67
B
HOH
69
3
HOH
HOH
69
B
HOH
70
3
HOH
HOH
70
B
HOH
71
3
HOH
HOH
71
B
HOH
72
3
HOH
HOH
72
B
HOH
73
3
HOH
HOH
73
B
HOH
75
3
HOH
HOH
75
B
HOH
76
3
HOH
HOH
76
B
HOH
77
3
HOH
HOH
77
B
HOH
80
3
HOH
HOH
80
B
HOH
81
3
HOH
HOH
81
B
HOH
82
3
HOH
HOH
82
B
HOH
84
3
HOH
HOH
84
B
HOH
89
3
HOH
HOH
89
B
HOH
94
3
HOH
HOH
94
B
HOH
95
3
HOH
HOH
95
B
HOH
96
3
HOH
HOH
96
B
C
1
n
1
DC
1
A
G
2
n
2
DG
2
A
C
3
n
3
DC
3
A
G
4
n
4
DG
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
C
9
n
9
DC
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
G
16
n
4
DG
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
C
21
n
9
DC
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
-4.72
0.40
104.50
99.78
A
A
A
O4'
C4'
C3'
DC
DC
DC
1
1
1
N
1
-12.54
1.80
114.10
101.56
A
A
A
C5'
C4'
C3'
DC
DC
DC
1
1
1
N
1
6.89
1.10
109.80
116.69
A
A
A
C5'
C4'
O4'
DC
DC
DC
1
1
1
N
1
1.91
0.30
108.30
110.21
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
3.94
0.60
119.90
123.84
A
A
A
N1
C6
O6
DG
DG
DG
2
2
2
N
1
-3.87
0.60
128.60
124.73
A
A
A
C5
C6
O6
DG
DG
DG
2
2
2
N
1
8.15
1.20
119.70
127.85
A
A
A
C3'
O3'
P
DG
DG
DC
2
2
3
Y
1
-13.48
1.60
120.90
107.42
A
A
A
P
O5'
C5'
DC
DC
DC
3
3
3
N
1
7.30
1.20
102.50
109.80
A
A
A
C3'
C2'
C1'
DC
DC
DC
3
3
3
N
1
3.38
0.50
119.90
123.28
A
A
A
C2
N3
C4
DC
DC
DC
3
3
3
N
1
-2.96
0.40
121.90
118.94
A
A
A
N3
C4
C5
DC
DC
DC
3
3
3
N
1
-11.44
1.20
119.70
108.26
A
A
A
C3'
O3'
P
DC
DC
DG
3
3
4
Y
1
-9.74
1.60
120.90
111.16
A
A
A
P
O5'
C5'
DG
DG
DG
4
4
4
N
1
5.30
0.30
108.30
113.60
A
A
A
O4'
C1'
N9
DG
DG
DG
4
4
4
N
1
-3.07
0.50
104.30
101.23
A
A
A
C5
N7
C8
DG
DG
DG
4
4
4
N
1
6.15
0.90
116.20
122.35
A
A
A
N1
C2
N2
DG
DG
DG
4
4
4
N
1
-5.75
0.60
128.60
122.85
A
A
A
C5
C6
O6
DG
DG
DG
4
4
4
N
1
-5.36
0.80
105.90
100.54
A
A
A
O4'
C1'
C2'
DA
DA
DA
5
5
5
N
1
3.85
0.30
108.30
112.15
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
-3.32
0.40
104.50
101.18
A
A
A
O4'
C4'
C3'
DA
DA
DA
6
6
6
N
1
-5.28
0.80
105.90
100.62
A
A
A
O4'
C1'
C2'
DA
DA
DA
6
6
6
N
1
-12.12
1.60
120.90
108.78
A
A
A
P
O5'
C5'
DT
DT
DT
7
7
7
N
1
1.97
0.30
108.30
110.27
A
A
A
O4'
C1'
N1
DT
DT
DT
7
7
7
N
1
-4.90
0.60
115.20
110.30
A
A
A
N3
C4
C5
DT
DT
DT
7
7
7
N
1
6.11
0.60
118.00
124.11
A
A
A
C4
C5
C6
DT
DT
DT
7
7
7
N
1
4.16
0.60
119.90
124.06
A
A
A
N3
C4
O4
DT
DT
DT
7
7
7
N
1
-4.60
0.60
119.00
114.40
A
A
A
C4
C5
C7
DT
DT
DT
7
7
7
N
1
-9.99
1.60
120.90
110.91
A
A
A
P
O5'
C5'
DT
DT
DT
8
8
8
N
1
-6.99
0.80
105.90
98.91
A
A
A
O4'
C1'
C2'
DT
DT
DT
8
8
8
N
1
4.39
0.60
114.60
118.99
A
A
A
N1
C2
N3
DT
DT
DT
8
8
8
N
1
4.70
0.60
118.00
122.70
A
A
A
C4
C5
C6
DT
DT
DT
8
8
8
N
1
-3.89
0.60
123.70
119.81
A
A
A
C5
C6
N1
DT
DT
DT
8
8
8
N
1
-6.09
0.60
122.30
116.21
A
A
A
N3
C2
O2
DT
DT
DT
8
8
8
N
1
-4.14
0.60
122.90
118.76
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
1
3.86
0.30
108.30
112.16
A
A
A
O4'
C1'
N1
DC
DC
DC
9
9
9
N
1
3.67
0.50
119.90
123.57
A
A
A
C2
N3
C4
DC
DC
DC
9
9
9
N
1
-2.57
0.40
121.90
119.33
A
A
A
N3
C4
C5
DC
DC
DC
9
9
9
N
1
6.36
0.60
118.90
125.26
A
A
A
N1
C2
O2
DC
DC
DC
9
9
9
N
1
-5.60
0.70
121.90
116.30
A
A
A
N3
C2
O2
DC
DC
DC
9
9
9
N
1
5.35
0.70
120.20
125.55
A
A
A
C5
C4
N4
DC
DC
DC
9
9
9
N
1
-5.22
0.80
102.40
97.18
A
A
A
C3'
C2'
C1'
DG
DG
DG
10
10
10
N
1
-9.86
1.60
120.90
111.04
A
A
A
P
O5'
C5'
DC
DC
DC
11
11
11
N
1
4.09
0.60
118.90
122.99
A
A
A
N1
C2
O2
DC
DC
DC
11
11
11
N
1
-5.07
0.70
121.90
116.83
A
A
A
N3
C2
O2
DC
DC
DC
11
11
11
N
1
-4.19
0.40
104.50
100.31
A
A
A
O4'
C4'
C3'
DG
DG
DG
12
12
12
N
1
5.80
0.30
108.30
114.10
A
A
A
O4'
C1'
N9
DG
DG
DG
12
12
12
N
1
-2.41
0.40
104.50
102.09
B
B
B
O4'
C4'
C3'
DC
DC
DC
13
13
13
N
1
3.98
0.60
118.90
122.88
B
B
B
N1
C2
O2
DC
DC
DC
13
13
13
N
1
3.69
0.30
108.30
111.99
B
B
B
O4'
C1'
N9
DG
DG
DG
14
14
14
N
1
-3.99
0.40
104.50
100.51
B
B
B
O4'
C4'
C3'
DC
DC
DC
15
15
15
N
1
4.87
0.70
110.30
115.17
B
B
B
C1'
O4'
C4'
DC
DC
DC
15
15
15
N
1
-7.40
0.80
105.90
98.50
B
B
B
O4'
C1'
C2'
DC
DC
DC
15
15
15
N
1
8.78
0.30
108.30
117.08
B
B
B
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
5.69
0.50
119.90
125.59
B
B
B
C2
N3
C4
DC
DC
DC
15
15
15
N
1
-5.39
0.40
121.90
116.51
B
B
B
N3
C4
C5
DC
DC
DC
15
15
15
N
1
3.33
0.50
121.00
124.33
B
B
B
C5
C6
N1
DC
DC
DC
15
15
15
N
1
6.36
0.70
118.00
124.36
B
B
B
N3
C4
N4
DC
DC
DC
15
15
15
N
1
2.65
0.30
108.30
110.95
B
B
B
O4'
C1'
N9
DG
DG
DG
16
16
16
N
1
5.84
0.70
110.30
116.14
B
B
B
C1'
O4'
C4'
DA
DA
DA
17
17
17
N
1
1.92
0.30
108.30
110.22
B
B
B
O4'
C1'
N9
DA
DA
DA
17
17
17
N
1
-5.96
0.40
104.50
98.54
B
B
B
O4'
C4'
C3'
DA
DA
DA
18
18
18
N
1
6.04
0.70
110.30
116.34
B
B
B
C1'
O4'
C4'
DA
DA
DA
18
18
18
N
1
-5.46
0.80
105.90
100.44
B
B
B
O4'
C1'
C2'
DA
DA
DA
18
18
18
N
1
3.55
0.30
108.30
111.85
B
B
B
O4'
C1'
N9
DA
DA
DA
18
18
18
N
1
-17.61
1.60
120.90
103.29
B
B
B
P
O5'
C5'
DT
DT
DT
19
19
19
N
1
8.89
0.30
108.30
117.19
B
B
B
O4'
C1'
N1
DT
DT
DT
19
19
19
N
1
-4.34
0.60
115.20
110.86
B
B
B
N3
C4
C5
DT
DT
DT
19
19
19
N
1
4.65
0.60
118.00
122.65
B
B
B
C4
C5
C6
DT
DT
DT
19
19
19
N
1
-7.57
0.60
122.90
115.33
B
B
B
C6
C5
C7
DT
DT
DT
19
19
19
N
1
-10.84
1.60
120.90
110.06
B
B
B
P
O5'
C5'
DT
DT
DT
20
20
20
N
1
-4.01
0.40
104.50
100.49
B
B
B
O4'
C4'
C3'
DT
DT
DT
20
20
20
N
1
-5.47
0.80
105.90
100.43
B
B
B
O4'
C1'
C2'
DT
DT
DT
20
20
20
N
1
-4.17
0.60
127.20
123.03
B
B
B
C2
N3
C4
DT
DT
DT
20
20
20
N
1
4.11
0.60
118.00
122.11
B
B
B
C4
C5
C6
DT
DT
DT
20
20
20
N
1
-3.84
0.60
123.70
119.86
B
B
B
C5
C6
N1
DT
DT
DT
20
20
20
N
1
-4.38
0.60
122.90
118.52
B
B
B
C6
C5
C7
DT
DT
DT
20
20
20
N
1
5.25
0.60
118.90
124.15
B
B
B
N1
C2
O2
DC
DC
DC
21
21
21
N
1
8.52
0.30
108.30
116.82
B
B
B
O4'
C1'
N9
DG
DG
DG
22
22
22
N
1
-12.60
1.90
104.00
91.40
B
B
B
O3'
P
O5'
DG
DC
DC
22
23
23
Y
1
4.10
0.60
106.00
110.10
B
B
B
O4'
C4'
C3'
DC
DC
DC
23
23
23
N
1
-4.97
0.70
102.20
97.23
B
B
B
C4'
C3'
C2'
DC
DC
DC
23
23
23
N
1
8.43
0.30
108.30
116.73
B
B
B
O4'
C1'
N1
DC
DC
DC
23
23
23
N
1
-9.74
1.60
120.90
111.16
B
B
B
P
O5'
C5'
DG
DG
DG
24
24
24
N
1
-13.77
1.90
112.60
98.83
B
B
B
N9
C1'
C2'
DG
DG
DG
24
24
24
N
1
11.53
0.30
108.30
119.83
B
B
B
O4'
C1'
N9
DG
DG
DG
24
24
24
N
1
A
A
C2'
C1'
DC
DC
1
1
-0.061
0.010
1.518
1.457
N
1
A
A
C5'
C4'
DC
DC
3
3
-0.080
0.011
1.509
1.429
N
1
A
A
N1
C2
DC
DC
3
3
-0.068
0.010
1.397
1.329
N
1
A
A
N3
C4
DA
DA
5
5
0.037
0.006
1.344
1.381
N
1
A
A
C5
N7
DA
DA
6
6
0.043
0.006
1.388
1.431
N
1
A
A
N9
C4
DA
DA
6
6
0.057
0.006
1.374
1.431
N
1
A
A
P
O5'
DT
DT
7
7
-0.063
0.010
1.593
1.530
N
1
A
A
C2'
C1'
DT
DT
7
7
-0.064
0.010
1.518
1.454
N
1
A
A
C6
N1
DT
DT
7
7
-0.045
0.007
1.378
1.333
N
1
A
A
P
O5'
DC
DC
9
9
-0.069
0.010
1.593
1.524
N
1
A
A
N1
C6
DC
DC
11
11
-0.044
0.006
1.367
1.323
N
1
A
A
P
O5'
DG
DG
12
12
0.069
0.010
1.593
1.662
N
1
A
A
N3
C4
DG
DG
12
12
0.044
0.007
1.350
1.394
N
1
B
B
C5'
C4'
DC
DC
13
13
0.062
0.007
1.512
1.574
N
1
B
B
N7
C8
DG
DG
14
14
-0.039
0.006
1.305
1.266
N
1
B
B
O3'
C3'
DC
DC
15
15
-0.049
0.006
1.419
1.370
N
1
B
B
C5
N7
DG
DG
16
16
-0.039
0.006
1.388
1.349
N
1
B
B
C2'
C1'
DT
DT
20
20
-0.072
0.010
1.518
1.446
N
1
B
B
O3'
C3'
DG
DG
22
22
-0.040
0.006
1.419
1.379
N
1
B
B
C6
N1
DG
DG
22
22
-0.047
0.007
1.391
1.344
N
1
B
B
C2
N2
DG
DG
22
22
-0.060
0.010
1.341
1.281
N
1
B
B
C3'
C2'
DG
DG
24
24
-0.050
0.008
1.516
1.466
N
0.1980000
0.1890000
0.1890000
2.200
8.000
3184
97.400
1
2.000
TR
isotropic
TR
isotropic
2.200
8.000
73
584
25
486
0
fix
fix
2.100
166D
9633
3846
1
refinement
X-PLOR
DRUG-DNA MINOR GROOVE RECOGNITION: CRYSTAL STRUCTURE OF GAMMA-OXAPENTAMIDINE COMPLEXED WITH D(CGCGAATTCGCG)2
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
DG
4
A
N1
DG
4
1_555
B
DC
21
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
N2
DG
4
1_555
B
DC
21
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
A
DG
4
A
O6
DG
4
1_555
B
DC
21
B
N4
DC
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
DC
9
A
N3
DC
9
1_555
B
DG
16
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
N4
DC
9
1_555
B
DG
16
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
A
DC
9
A
O2
DC
9
1_555
B
DG
16
B
N2
DG
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
166D
PDB
1
166D
1
12
166D
1
12
166D
A
1
1
12
13
24
166D
13
24
166D
B
1
1
12
BINDING SITE FOR RESIDUE PET B 25
B
PET
25
Software
13
A
DA
5
A
DA
5
13
1_555
A
DA
6
A
DA
6
13
1_555
A
DT
7
A
DT
7
13
1_555
A
DT
8
A
DT
8
13
1_555
A
DC
9
A
DC
9
13
1_555
B
DA
18
B
DA
6
13
1_555
B
DT
19
B
DT
7
13
1_555
B
DT
20
B
DT
8
13
1_555
B
DC
21
B
DC
9
13
1_555
B
HOH
45
E
HOH
13
1_555
B
HOH
69
E
HOH
13
1_555
B
HOH
81
E
HOH
13
1_555
B
HOH
82
E
HOH
13
1_555
19
P 21 21 21