0.019798
0.011430
0.000000
0.000000
0.022861
0.000000
0.000000
0.000000
0.019335
0.00000
0.00000
0.00000
Collie, G.W.
Neidle, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
50.510
50.510
51.720
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
H2 O
18.015
WATER
non-polymer
K 1
39.098
POTASSIUM ION
non-polymer
C46 H72 N12 O4
857.142
2,7-bis[3-(4-methylpiperazin-1-yl)propyl]-4,9-bis{[3-(4-methylpiperazin-1-yl)propyl]amino}benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone
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
Y
49
N
N
Y
50
N
C
Y
51
N
N
Y
52
N
C
N
53
N
C
N
54
N
O
N
55
N
N
N
56
N
C
N
57
N
N
N
58
N
N
Y
59
N
C
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
H
N
72
N
H
N
73
N
H
N
74
N
O
N
75
N
P
N
76
N
O
N
77
N
O
N
78
N
O
N
79
N
C
N
80
R
C
N
81
N
O
N
82
S
C
N
83
N
O
N
84
N
C
N
85
R
C
N
86
N
N
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
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
H
N
109
N
H
N
110
N
O
N
111
N
H
N
112
N
H
N
113
N
K
N
114
N
C
N
115
N
C
N
116
N
C
N
117
N
C
N
118
N
O
N
119
N
O
N
120
N
O
N
121
N
O
Y
122
N
C
Y
123
N
C
N
124
N
C
N
125
N
C
N
126
N
C
N
127
N
C
N
128
N
C
N
129
N
C
N
130
N
C
N
131
N
C
N
132
N
C
N
133
N
C
N
134
N
C
N
135
N
C
N
136
N
C
N
137
N
C
N
138
N
C
N
139
N
C
N
140
N
C
N
141
N
C
N
142
N
C
N
143
N
C
N
144
N
C
N
145
N
C
N
146
N
C
N
147
N
C
N
148
N
C
N
149
N
C
N
150
N
C
N
151
N
C
N
152
N
N
N
153
N
N
Y
154
N
C
Y
155
N
C
N
156
N
C
N
157
N
C
N
158
N
C
N
159
N
C
Y
160
N
C
Y
161
N
C
Y
162
N
C
Y
163
N
C
Y
164
N
C
Y
165
N
C
N
166
N
N
N
167
N
N
N
168
N
N
N
169
N
N
N
170
N
N
N
171
N
N
N
172
N
N
N
173
N
N
N
174
N
N
N
175
N
N
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
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
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
Y
62
N
sing
Y
63
N
sing
Y
64
N
doub
N
65
N
sing
Y
66
N
sing
N
67
N
sing
Y
68
N
doub
N
69
N
doub
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
doub
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
doub
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
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
doub
N
108
N
sing
N
109
N
sing
N
110
N
doub
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
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
doub
Y
135
N
doub
Y
136
N
sing
Y
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
doub
N
142
N
sing
N
143
N
sing
Y
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
Y
148
N
doub
N
149
N
sing
N
150
N
sing
N
151
N
sing
Y
152
N
sing
Y
153
N
sing
Y
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
doub
Y
161
N
doub
N
162
N
sing
Y
163
N
doub
N
164
N
doub
Y
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
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
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
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
US
J.Med.Chem.
JMCMAR
0151
0022-2623
56
2959
2974
10.1021/jm301899y
23514618
Structure-based design and evaluation of naphthalene diimide g-quadruplex ligands as telomere targeting agents in pancreatic cancer cells.
2013
10.2210/pdb4daq/pdb
pdb_00004daq
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2011-12-16
ADSC QUANTUM 315r
Si 111 CHANNEL
SINGLE WAVELENGTH
M
x-ray
1
0.9795
1.0
I04
Diamond
0.9795
SYNCHROTRON
DIAMOND BEAMLINE I04
6670.290
DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
1
syn
polymer
39.098
POTASSIUM ION
3
syn
non-polymer
857.142
2,7-bis[3-(4-methylpiperazin-1-yl)propyl]-4,9-bis{[3-(4-methylpiperazin-1-yl)propyl]amino}benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone
1
syn
non-polymer
18.015
water
8
nat
water
no
no
(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)
(DG)
GGGTTAGGGTTAGGGTTAGGG
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
2.86
56.92
VAPOR DIFFUSION, HANGING DROP
6.5
15% PEG400, 150 mM sodium chloride and 50 mM sodium cacodylate (pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 285K
285
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Database references
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-01-16
1
1
2013-04-03
1
2
2013-04-24
1
3
2023-09-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Similar naphthalene diimide compound bound to the same 21-mer human telomeric G-quadruplex.
Same naphthalene diimide compound bound to a 22-mer human telomeric G-quadruplex.
Similar naphthalene diimide compound bound to a 22-mer human telomeric G-quadruplex.
Similar naphthalene diimide compound bound to a 22-mer human telomeric G-quadruplex.
RCSB
Y
RCSB
2012-01-13
REL
REL
K
POTASSIUM ION
R8G
2,7-bis[3-(4-methylpiperazin-1-yl)propyl]-4,9-bis{[3-(4-methylpiperazin-1-yl)propyl]amino}benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone
HOH
water
DNA synthesized by standard phosphoramidite chemistry.
32630
Synthetic DNA
sample
3SC8
PDB ENTRY 3SC8
PDB
experimental model
K
1
2
K
K
101
A
K
2
2
K
K
102
A
K
3
2
K
K
103
A
R8G
23
3
R8G
R8G
104
A
HOH
1
4
HOH
HOH
201
A
HOH
2
4
HOH
HOH
202
A
HOH
3
4
HOH
HOH
203
A
HOH
4
4
HOH
HOH
204
A
HOH
5
4
HOH
HOH
205
A
HOH
6
4
HOH
HOH
206
A
HOH
7
4
HOH
HOH
207
A
HOH
8
4
HOH
HOH
208
A
DG
1
n
1
DG
1
A
DG
2
n
2
DG
2
A
DG
3
n
3
DG
3
A
DT
4
n
4
DT
4
A
DT
5
n
5
DT
5
A
DA
6
n
6
DA
6
A
DG
7
n
7
DG
7
A
DG
8
n
8
DG
8
A
DG
9
n
9
DG
9
A
DT
10
n
10
DT
10
A
DT
11
n
11
DT
11
A
DA
12
n
12
DA
12
A
DG
13
n
13
DG
13
A
DG
14
n
14
DG
14
A
DG
15
n
15
DG
15
A
DT
16
n
16
DT
16
A
DT
17
n
17
DT
17
A
DA
18
n
18
DA
18
A
DG
19
n
19
DG
19
A
DG
20
n
20
DG
20
A
DG
21
n
21
DG
21
A
author_and_software_defined_assembly
PISA
1
monomeric
A
DG
1
A
O6
DG
1
1_555
A
K
102
C
K
K
1_555
A
DG
2
A
O6
DG
2
1_555
72.9
A
DG
1
A
O6
DG
1
1_555
A
K
102
C
K
K
1_555
A
DG
7
A
O6
DG
7
1_555
63.6
A
DG
2
A
O6
DG
2
1_555
A
K
102
C
K
K
1_555
A
DG
7
A
O6
DG
7
1_555
94.3
A
DG
1
A
O6
DG
1
1_555
A
K
102
C
K
K
1_555
A
DG
8
A
O6
DG
8
1_555
135.1
A
DG
2
A
O6
DG
2
1_555
A
K
102
C
K
K
1_555
A
DG
8
A
O6
DG
8
1_555
80.7
A
DG
7
A
O6
DG
7
1_555
A
K
102
C
K
K
1_555
A
DG
8
A
O6
DG
8
1_555
83.4
A
DG
1
A
O6
DG
1
1_555
A
K
102
C
K
K
1_555
A
DG
13
A
O6
DG
13
1_555
95.6
A
DG
2
A
O6
DG
2
1_555
A
K
102
C
K
K
1_555
A
DG
13
A
O6
DG
13
1_555
152.8
A
DG
7
A
O6
DG
7
1_555
A
K
102
C
K
K
1_555
A
DG
13
A
O6
DG
13
1_555
58.7
A
DG
8
A
O6
DG
8
1_555
A
K
102
C
K
K
1_555
A
DG
13
A
O6
DG
13
1_555
91.6
A
DG
1
A
O6
DG
1
1_555
A
K
102
C
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
155.6
A
DG
2
A
O6
DG
2
1_555
A
K
102
C
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
116.8
A
DG
7
A
O6
DG
7
1_555
A
K
102
C
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
133.1
A
DG
8
A
O6
DG
8
1_555
A
K
102
C
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
69.2
A
DG
13
A
O6
DG
13
1_555
A
K
102
C
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
83.9
A
DG
1
A
O6
DG
1
1_555
A
K
102
C
K
K
1_555
A
DG
19
A
O6
DG
19
1_555
65.2
A
DG
2
A
O6
DG
2
1_555
A
K
102
C
K
K
1_555
A
DG
19
A
O6
DG
19
1_555
127.6
A
DG
7
A
O6
DG
7
1_555
A
K
102
C
K
K
1_555
A
DG
19
A
O6
DG
19
1_555
93.9
A
DG
8
A
O6
DG
8
1_555
A
K
102
C
K
K
1_555
A
DG
19
A
O6
DG
19
1_555
151.7
A
DG
13
A
O6
DG
13
1_555
A
K
102
C
K
K
1_555
A
DG
19
A
O6
DG
19
1_555
63.6
A
DG
14
A
O6
DG
14
1_555
A
K
102
C
K
K
1_555
A
DG
19
A
O6
DG
19
1_555
93.3
A
DG
1
A
O6
DG
1
1_555
A
K
102
C
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
89.3
A
DG
2
A
O6
DG
2
1_555
A
K
102
C
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
70.8
A
DG
7
A
O6
DG
7
1_555
A
K
102
C
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
152.2
A
DG
8
A
O6
DG
8
1_555
A
K
102
C
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
115.6
A
DG
13
A
O6
DG
13
1_555
A
K
102
C
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
134.9
A
DG
14
A
O6
DG
14
1_555
A
K
102
C
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
74.5
A
DG
19
A
O6
DG
19
1_555
A
K
102
C
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
78.5
A
DG
1
A
O6
DG
1
1_555
A
K
103
D
K
K
1_555
A
DG
7
A
O6
DG
7
1_555
63.1
A
DG
1
A
O6
DG
1
1_555
A
K
103
D
K
K
1_555
A
DG
13
A
O6
DG
13
1_555
108.5
A
DG
7
A
O6
DG
7
1_555
A
K
103
D
K
K
1_555
A
DG
13
A
O6
DG
13
1_555
71.5
A
DG
1
A
O6
DG
1
1_555
A
K
103
D
K
K
1_555
A
DG
19
A
O6
DG
19
1_555
64.0
A
DG
7
A
O6
DG
7
1_555
A
K
103
D
K
K
1_555
A
DG
19
A
O6
DG
19
1_555
101.7
A
DG
13
A
O6
DG
13
1_555
A
K
103
D
K
K
1_555
A
DG
19
A
O6
DG
19
1_555
75.6
A
DG
2
A
O6
DG
2
1_555
A
K
101
B
K
K
1_555
A
DG
3
A
O6
DG
3
1_555
66.5
A
DG
2
A
O6
DG
2
1_555
A
K
101
B
K
K
1_555
A
DG
8
A
O6
DG
8
1_555
69.1
A
DG
3
A
O6
DG
3
1_555
A
K
101
B
K
K
1_555
A
DG
8
A
O6
DG
8
1_555
90.1
A
DG
2
A
O6
DG
2
1_555
A
K
101
B
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
123.4
A
DG
3
A
O6
DG
3
1_555
A
K
101
B
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
80.6
A
DG
8
A
O6
DG
8
1_555
A
K
101
B
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
66.3
A
DG
2
A
O6
DG
2
1_555
A
K
101
B
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
99.6
A
DG
3
A
O6
DG
3
1_555
A
K
101
B
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
148.3
A
DG
8
A
O6
DG
8
1_555
A
K
101
B
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
58.2
A
DG
9
A
O6
DG
9
1_555
A
K
101
B
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
85.0
A
DG
2
A
O6
DG
2
1_555
A
K
101
B
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
154.8
A
DG
3
A
O6
DG
3
1_555
A
K
101
B
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
137.7
A
DG
8
A
O6
DG
8
1_555
A
K
101
B
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
110.6
A
DG
9
A
O6
DG
9
1_555
A
K
101
B
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
75.4
A
DG
14
A
O6
DG
14
1_555
A
K
101
B
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
63.0
A
DG
2
A
O6
DG
2
1_555
A
K
101
B
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
65.4
A
DG
3
A
O6
DG
3
1_555
A
K
101
B
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
124.4
A
DG
8
A
O6
DG
8
1_555
A
K
101
B
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
97.4
A
DG
9
A
O6
DG
9
1_555
A
K
101
B
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
151.6
A
DG
14
A
O6
DG
14
1_555
A
K
101
B
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
66.6
A
DG
15
A
O6
DG
15
1_555
A
K
101
B
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
90.1
A
DG
2
A
O6
DG
2
1_555
A
K
101
B
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
91.6
A
DG
3
A
O6
DG
3
1_555
A
K
101
B
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
83.2
A
DG
8
A
O6
DG
8
1_555
A
K
101
B
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
160.6
A
DG
9
A
O6
DG
9
1_555
A
K
101
B
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
129.8
A
DG
14
A
O6
DG
14
1_555
A
K
101
B
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
126.9
A
DG
15
A
O6
DG
15
1_555
A
K
101
B
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
86.1
A
DG
20
A
O6
DG
20
1_555
A
K
101
B
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
71.9
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
K
103
D
K
1
8.99
1.20
119.70
128.69
A
A
A
C3'
O3'
P
DT
DT
DT
10
10
11
Y
51.950
-0.02
-0.01
0.00
-0.02
0.00
0.03
0.945
0.913
HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
0.27531
0.21172
0.21555
2.754
22.69
123
1995
1995
5.8
99.02
15.368
0.294
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.395
0.80
0.80
1.20
PDB ENTRY 3SC8
MAXIMUM LIKELIHOOD
MASK
2.754
22.69
8
517
65
444
0
0.007
0.012
569
1.588
1.512
873
0.061
0.200
63
0.008
0.020
261
0.419
0.465
2.825
3
132
20
100.00
91.91
2.69
25.86
4DAQ
2284
2284
2
2
0.047
1
24.8
7.3
99.2
0.613
2.69
2.76
2.9
168
1
7.7
100
data collection
DNA
phasing
PHASER
refinement
REFMAC
5.6.0117
data reduction
xia2
data scaling
SCALA
Crystal structure of an intramolecular human telomeric DNA G-quadruplex 21-mer bound by the naphthalene diimide compound BMSG-SH-3
1
N
N
2
N
N
2
N
N
2
N
N
3
N
N
4
N
N
metalc
2.675
A
DG
1
A
O6
DG
1
1_555
A
K
102
C
K
K
1_555
metalc
2.897
A
DG
1
A
O6
DG
1
1_555
A
K
103
D
K
K
1_555
metalc
2.818
A
DG
2
A
O6
DG
2
1_555
A
K
101
B
K
K
1_555
metalc
2.594
A
DG
2
A
O6
DG
2
1_555
A
K
102
C
K
K
1_555
metalc
2.674
A
DG
3
A
O6
DG
3
1_555
A
K
101
B
K
K
1_555
metalc
2.804
A
DG
7
A
O6
DG
7
1_555
A
K
102
C
K
K
1_555
metalc
2.598
A
DG
7
A
O6
DG
7
1_555
A
K
103
D
K
K
1_555
metalc
2.993
A
DG
8
A
O6
DG
8
1_555
A
K
101
B
K
K
1_555
metalc
2.497
A
DG
8
A
O6
DG
8
1_555
A
K
102
C
K
K
1_555
metalc
2.753
A
DG
9
A
O6
DG
9
1_555
A
K
101
B
K
K
1_555
metalc
3.333
A
DG
13
A
O6
DG
13
1_555
A
K
102
C
K
K
1_555
metalc
2.612
A
DG
13
A
O6
DG
13
1_555
A
K
103
D
K
K
1_555
metalc
3.053
A
DG
14
A
O6
DG
14
1_555
A
K
101
B
K
K
1_555
metalc
2.674
A
DG
14
A
O6
DG
14
1_555
A
K
102
C
K
K
1_555
metalc
2.776
A
DG
15
A
O6
DG
15
1_555
A
K
101
B
K
K
1_555
metalc
2.899
A
DG
19
A
O6
DG
19
1_555
A
K
102
C
K
K
1_555
metalc
2.775
A
DG
19
A
O6
DG
19
1_555
A
K
103
D
K
K
1_555
metalc
2.804
A
DG
20
A
O6
DG
20
1_555
A
K
101
B
K
K
1_555
metalc
2.651
A
DG
20
A
O6
DG
20
1_555
A
K
102
C
K
K
1_555
metalc
2.615
A
DG
21
A
O6
DG
21
1_555
A
K
101
B
K
K
1_555
hydrog
TYPE_6_PAIR
A
DG
1
A
N1
DG
1
1_555
A
DG
7
A
O6
DG
7
1_555
hydrog
TYPE_6_PAIR
A
DG
1
A
N2
DG
1
1_555
A
DG
7
A
N7
DG
7
1_555
hydrog
TYPE_6_PAIR
A
DG
1
A
N7
DG
1
1_555
A
DG
19
A
N2
DG
19
1_555
hydrog
TYPE_6_PAIR
A
DG
1
A
O6
DG
1
1_555
A
DG
19
A
N1
DG
19
1_555
hydrog
TYPE_6_PAIR
A
DG
2
A
N1
DG
2
1_555
A
DG
8
A
O6
DG
8
1_555
hydrog
TYPE_6_PAIR
A
DG
2
A
N2
DG
2
1_555
A
DG
8
A
N7
DG
8
1_555
hydrog
TYPE_6_PAIR
A
DG
2
A
N7
DG
2
1_555
A
DG
20
A
N2
DG
20
1_555
hydrog
TYPE_6_PAIR
A
DG
2
A
O6
DG
2
1_555
A
DG
20
A
N1
DG
20
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
N1
DG
3
1_555
A
DG
9
A
O6
DG
9
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
N2
DG
3
1_555
A
DG
9
A
N7
DG
9
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
N7
DG
3
1_555
A
DG
21
A
N2
DG
21
1_555
hydrog
TYPE_6_PAIR
A
DG
3
A
O6
DG
3
1_555
A
DG
21
A
N1
DG
21
1_555
hydrog
TYPE_6_PAIR
A
DG
7
A
N1
DG
7
1_555
A
DG
13
A
O6
DG
13
1_555
hydrog
TYPE_6_PAIR
A
DG
7
A
N2
DG
7
1_555
A
DG
13
A
N7
DG
13
1_555
hydrog
TYPE_6_PAIR
A
DG
8
A
N1
DG
8
1_555
A
DG
14
A
O6
DG
14
1_555
hydrog
TYPE_6_PAIR
A
DG
8
A
N2
DG
8
1_555
A
DG
14
A
N7
DG
14
1_555
hydrog
TYPE_6_PAIR
A
DG
9
A
N1
DG
9
1_555
A
DG
15
A
O6
DG
15
1_555
hydrog
TYPE_6_PAIR
A
DG
9
A
N2
DG
9
1_555
A
DG
15
A
N7
DG
15
1_555
hydrog
TYPE_6_PAIR
A
DG
13
A
N1
DG
13
1_555
A
DG
19
A
O6
DG
19
1_555
hydrog
TYPE_6_PAIR
A
DG
13
A
N2
DG
13
1_555
A
DG
19
A
N7
DG
19
1_555
hydrog
TYPE_6_PAIR
A
DG
14
A
N1
DG
14
1_555
A
DG
20
A
O6
DG
20
1_555
hydrog
TYPE_6_PAIR
A
DG
14
A
N2
DG
14
1_555
A
DG
20
A
N7
DG
20
1_555
hydrog
TYPE_6_PAIR
A
DG
15
A
N1
DG
15
1_555
A
DG
21
A
O6
DG
21
1_555
hydrog
TYPE_6_PAIR
A
DG
15
A
N2
DG
15
1_555
A
DG
21
A
N7
DG
21
1_555
DNA
intramolecular, ligand-complex, G-quadruplex, DNA
4DAQ
PDB
1
1
4DAQ
GGGTTAGGGTTAGGGTTAGGG
1
21
4DAQ
1
21
4DAQ
A
1
1
21
BINDING SITE FOR RESIDUE K A 101
A
K
101
Software
9
BINDING SITE FOR RESIDUE K A 102
A
K
102
Software
11
BINDING SITE FOR RESIDUE K A 103
A
K
103
Software
10
BINDING SITE FOR RESIDUE R8G A 104
A
R8G
104
Software
9
A
DG
2
A
DG
2
9
1_555
A
DG
3
A
DG
3
9
1_555
A
DG
8
A
DG
8
9
1_555
A
DG
9
A
DG
9
9
1_555
A
DG
14
A
DG
14
9
1_555
A
DG
15
A
DG
15
9
1_555
A
DG
20
A
DG
20
9
1_555
A
DG
21
A
DG
21
9
1_555
A
K
102
C
K
9
1_555
A
DG
1
A
DG
1
11
1_555
A
DG
2
A
DG
2
11
1_555
A
DG
7
A
DG
7
11
1_555
A
DG
8
A
DG
8
11
1_555
A
DG
13
A
DG
13
11
1_555
A
DG
14
A
DG
14
11
1_555
A
DG
19
A
DG
19
11
1_555
A
DG
20
A
DG
20
11
1_555
A
K
101
B
K
11
1_555
A
K
103
D
K
11
4_555
A
K
103
D
K
11
1_555
A
DG
1
A
DG
1
10
4_555
A
DG
1
A
DG
1
10
1_555
A
DG
7
A
DG
7
10
1_555
A
DG
7
A
DG
7
10
4_555
A
DG
13
A
DG
13
10
1_555
A
DG
13
A
DG
13
10
4_555
A
DG
19
A
DG
19
10
4_555
A
DG
19
A
DG
19
10
1_555
A
K
102
C
K
10
1_555
A
K
102
C
K
10
4_555
A
DG
3
A
DG
3
9
1_555
A
DT
4
A
DT
4
9
1_555
A
DT
5
A
DT
5
9
2_655
A
DG
9
A
DG
9
9
1_555
A
DT
10
A
DT
10
9
1_555
A
DT
11
A
DT
11
9
6_655
A
DA
12
A
DA
12
9
6_655
A
DG
15
A
DG
15
9
1_555
A
DG
21
A
DG
21
9
1_555
152
P 31 2 1