0.019470
0.011241
0.000000
0.000000
0.022482
0.000000
0.000000
0.000000
0.019331
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
51.360
51.360
51.730
C44 H66 N10 O6
831.058
4,9-bis{[3-(4-methylpiperazin-1-yl)propyl]amino}-2,7-bis[3-(morpholin-4-yl)propyl]benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone
non-polymer
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
N
1
N
C
N
2
N
C
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
O
Y
7
N
C
Y
8
N
C
N
9
N
C
N
10
N
C
N
11
N
C
N
12
N
C
N
13
N
C
N
14
N
C
N
15
N
C
N
16
N
C
N
17
N
C
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
C
N
22
N
C
N
23
N
C
N
24
N
C
N
25
N
C
N
26
N
C
N
27
N
C
N
28
N
C
N
29
N
C
N
30
N
C
N
31
N
C
N
32
N
C
N
33
N
C
N
34
N
C
N
35
N
C
N
36
N
C
N
37
N
N
N
38
N
N
Y
39
N
C
Y
40
N
C
N
41
N
C
N
42
N
C
N
43
N
C
N
44
N
C
Y
45
N
C
Y
46
N
C
Y
47
N
C
Y
48
N
C
Y
49
N
C
Y
50
N
C
N
51
N
N
N
52
N
N
N
53
N
O
N
54
N
O
N
55
N
N
N
56
N
N
N
57
N
N
N
58
N
N
N
59
N
N
N
60
N
N
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
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
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
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
O
N
128
N
P
N
129
N
O
N
130
N
O
N
131
N
O
N
132
N
C
N
133
R
C
N
134
N
O
N
135
S
C
N
136
N
O
N
137
N
C
N
138
R
C
Y
139
N
N
Y
140
N
C
Y
141
N
N
Y
142
N
C
Y
143
N
C
N
144
N
N
Y
145
N
N
Y
146
N
C
Y
147
N
N
Y
148
N
C
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
O
N
164
N
P
N
165
N
O
N
166
N
O
N
167
N
O
N
168
N
C
N
169
R
C
N
170
N
O
N
171
S
C
N
172
N
O
N
173
N
C
N
174
R
C
Y
175
N
N
Y
176
N
C
Y
177
N
N
Y
178
N
C
N
179
N
C
N
180
N
O
N
181
N
N
N
182
N
C
N
183
N
N
N
184
N
N
Y
185
N
C
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
O
N
201
N
P
N
202
N
O
N
203
N
O
N
204
N
O
N
205
N
C
N
206
R
C
N
207
N
O
N
208
S
C
N
209
N
O
N
210
N
C
N
211
R
C
N
212
N
N
N
213
N
C
N
214
N
O
N
215
N
N
N
216
N
C
N
217
N
O
N
218
N
C
N
219
N
C
N
220
N
C
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
O
N
237
N
H
N
238
N
H
N
239
N
K
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
doub
N
10
N
doub
N
11
N
doub
N
12
N
doub
Y
13
N
doub
Y
14
N
sing
N
15
N
sing
Y
16
N
doub
Y
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
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
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
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
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
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
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
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
Y
119
N
doub
Y
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
Y
129
N
doub
Y
130
N
sing
Y
131
N
sing
Y
132
N
doub
Y
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
doub
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
Y
157
N
sing
Y
158
N
sing
Y
159
N
doub
N
160
N
sing
Y
161
N
sing
Y
162
N
sing
Y
163
N
doub
N
164
N
sing
Y
165
N
doub
N
166
N
sing
N
167
N
sing
Y
168
N
sing
Y
169
N
doub
N
170
N
sing
Y
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
doub
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
Y
195
N
sing
Y
196
N
sing
Y
197
N
doub
N
198
N
sing
Y
199
N
sing
N
200
N
sing
Y
201
N
doub
N
202
N
doub
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
doub
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
doub
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
doub
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
doub
N
241
N
sing
N
242
N
sing
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
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/pdb3uyh/pdb
pdb_00003uyh
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
2011-12-05
ADSC QUANTUM 315r
SI 111 CHANNEL
SINGLE WAVELENGTH
M
x-ray
1
0.9795
1.0
I04
Diamond
0.9795
SYNCHROTRON
DIAMOND BEAMLINE I04
6983.497
human telomeric DNA sequence
1
syn
polymer
39.098
POTASSIUM ION
3
syn
non-polymer
831.058
4,9-bis{[3-(4-methylpiperazin-1-yl)propyl]amino}-2,7-bis[3-(morpholin-4-yl)propyl]benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone
1
syn
non-polymer
18.015
water
51
nat
water
no
no
(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)
(DG)(DG)
AGGGTTAGGGTTAGGGTTAGGG
A
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
1
2.83
56.60
VAPOR DIFFUSION, HANGING DROP
6.5
15% PEG400, 100 mM sodium chloride, 100 mM lithium chloride, 100 mM potassium bromide, 50 mM sodium cacodylate (pH 6.5)., VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
-0.464
3
6
A
8
A
14
-92.257
A_DG8:DG14_A
1
-10.143
1.439
0.256
3.453
0.713
3
6
A
9
A
15
-94.314
A_DG9:DG15_A
2
-5.350
1.601
-0.033
3.273
6.554
3
6
A
10
A
16
-89.862
A_DG10:DG16_A
3
-11.895
1.619
0.107
3.458
-7.980
3
6
A
4
A
22
87.977
A_DG4:DG22_A
4
7.859
-1.838
-0.054
-3.398
-4.393
3
6
A
3
A
21
92.758
A_DG3:DG21_A
5
0.412
-1.554
0.456
-3.386
1.469
3
6
A
2
A
20
88.051
A_DG2:DG20_A
6
-3.571
-1.589
0.346
-3.892
3.345
32.875
A
A
8
9
-1.184
A
A
14
15
3.337
-0.670
-0.537
-0.828
AA_DG8DG9:DG15DG14_AA
1
0.461
-0.815
32.865
-1.347
1.030
2.798
26.001
A
A
9
10
18.964
A
A
15
16
3.173
8.383
-0.687
-0.580
AA_DG9DG10:DG16DG15_AA
2
0.958
-2.167
24.616
-3.453
1.774
0.351
-179.629
A
A
10
4
4.555
A
A
16
22
0.351
-9.110
1.619
3.479
AA_DG10DG4:DG22DG16_AA
3
12.305
6.153
-179.625
-1.739
0.810
-2.969
-26.108
A
A
4
3
16.165
A
A
22
21
-3.309
-7.209
0.562
0.705
AA_DG4DG3:DG21DG22_AA
4
-1.022
-2.293
-25.089
-3.485
1.517
-3.213
-34.103
A
A
3
2
3.037
A
A
21
20
-3.267
-1.779
0.135
0.740
AA_DG3DG2:DG20DG21_AA
5
-1.858
-3.171
-34.009
-1.542
0.523
software
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
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-01-02
1
1
2013-04-03
1
2
2013-04-24
1
3
2017-11-08
1
4
2023-09-13
_software.name
_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.ptnr2_auth_seq_id
_pdbx_struct_conn_angle.ptnr2_label_asym_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
Same G-quadruplex bound by a similar naphthalene diimide-based ligand.
Same G-quadruplex bound by a similar naphthalene diimide-based ligand.
12-mer G-quadruplex bound by a naphthalene diimide-based ligand.
23-mer G-quadruplex bound by a naphthalene diimide-based ligand.
RCSB
Y
RCSB
2011-12-06
REL
REL
K
POTASSIUM ION
0DX
4,9-bis{[3-(4-methylpiperazin-1-yl)propyl]amino}-2,7-bis[3-(morpholin-4-yl)propyl]benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone
HOH
water
DNA synthesised 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
0DX
23
3
0DX
0DX
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
HOH
9
4
HOH
HOH
209
A
HOH
10
4
HOH
HOH
210
A
HOH
11
4
HOH
HOH
211
A
HOH
12
4
HOH
HOH
212
A
HOH
13
4
HOH
HOH
213
A
HOH
14
4
HOH
HOH
214
A
HOH
15
4
HOH
HOH
215
A
HOH
16
4
HOH
HOH
216
A
HOH
17
4
HOH
HOH
217
A
HOH
18
4
HOH
HOH
218
A
HOH
19
4
HOH
HOH
219
A
HOH
20
4
HOH
HOH
220
A
HOH
21
4
HOH
HOH
221
A
HOH
22
4
HOH
HOH
222
A
HOH
23
4
HOH
HOH
223
A
HOH
24
4
HOH
HOH
224
A
HOH
25
4
HOH
HOH
225
A
HOH
26
4
HOH
HOH
226
A
HOH
27
4
HOH
HOH
227
A
HOH
28
4
HOH
HOH
228
A
HOH
29
4
HOH
HOH
229
A
HOH
30
4
HOH
HOH
230
A
HOH
31
4
HOH
HOH
231
A
HOH
32
4
HOH
HOH
232
A
HOH
33
4
HOH
HOH
233
A
HOH
34
4
HOH
HOH
234
A
HOH
35
4
HOH
HOH
235
A
HOH
36
4
HOH
HOH
236
A
HOH
37
4
HOH
HOH
237
A
HOH
38
4
HOH
HOH
238
A
HOH
39
4
HOH
HOH
239
A
HOH
40
4
HOH
HOH
240
A
HOH
41
4
HOH
HOH
241
A
HOH
42
4
HOH
HOH
242
A
HOH
43
4
HOH
HOH
243
A
HOH
44
4
HOH
HOH
244
A
HOH
45
4
HOH
HOH
245
A
HOH
46
4
HOH
HOH
246
A
HOH
47
4
HOH
HOH
247
A
HOH
48
4
HOH
HOH
248
A
HOH
49
4
HOH
HOH
249
A
HOH
50
4
HOH
HOH
250
A
HOH
51
4
HOH
HOH
251
A
n
1
1
A
DG
2
n
2
DG
2
A
DG
3
n
3
DG
3
A
DG
4
n
4
DG
4
A
DT
5
n
5
DT
5
A
DT
6
n
6
DT
6
A
DA
7
n
7
DA
7
A
DG
8
n
8
DG
8
A
DG
9
n
9
DG
9
A
DG
10
n
10
DG
10
A
DT
11
n
11
DT
11
A
DT
12
n
12
DT
12
A
DA
13
n
13
DA
13
A
DG
14
n
14
DG
14
A
DG
15
n
15
DG
15
A
DG
16
n
16
DG
16
A
DT
17
n
17
DT
17
A
DT
18
n
18
DT
18
A
DA
19
n
19
DA
19
A
DG
20
n
20
DG
20
A
DG
21
n
21
DG
21
A
DG
22
n
22
DG
22
A
author_and_software_defined_assembly
PISA
1
monomeric
A
DG
2
A
O6
DG
2
1_555
A
K
102
C
K
K
1_555
A
DG
3
A
O6
DG
3
1_555
73.0
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
70.0
A
DG
3
A
O6
DG
3
1_555
A
K
102
C
K
K
1_555
A
DG
8
A
O6
DG
8
1_555
89.5
A
DG
2
A
O6
DG
2
1_555
A
K
102
C
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
130.3
A
DG
3
A
O6
DG
3
1_555
A
K
102
C
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
71.4
A
DG
8
A
O6
DG
8
1_555
A
K
102
C
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
76.1
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
107.9
A
DG
3
A
O6
DG
3
1_555
A
K
102
C
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
154.7
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
68.0
A
DG
9
A
O6
DG
9
1_555
A
K
102
C
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
91.1
A
DG
2
A
O6
DG
2
1_555
A
K
102
C
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
156.7
A
DG
3
A
O6
DG
3
1_555
A
K
102
C
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
111.0
A
DG
8
A
O6
DG
8
1_555
A
K
102
C
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
131.7
A
DG
9
A
O6
DG
9
1_555
A
K
102
C
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
70.5
A
DG
14
A
O6
DG
14
1_555
A
K
102
C
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
78.5
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
71.9
A
DG
3
A
O6
DG
3
1_555
A
K
102
C
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
132.2
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
107.5
A
DG
9
A
O6
DG
9
1_555
A
K
102
C
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
155.1
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
68.7
A
DG
15
A
O6
DG
15
1_555
A
K
102
C
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
90.7
A
DG
2
A
O6
DG
2
1_555
A
K
102
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
88.0
A
DG
3
A
O6
DG
3
1_555
A
K
102
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
71.2
A
DG
8
A
O6
DG
8
1_555
A
K
102
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
154.4
A
DG
9
A
O6
DG
9
1_555
A
K
102
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
111.6
A
DG
14
A
O6
DG
14
1_555
A
K
102
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
133.6
A
DG
15
A
O6
DG
15
1_555
A
K
102
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
72.6
A
DG
20
A
O6
DG
20
1_555
A
K
102
C
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
76.1
A
DG
2
A
O6
DG
2
1_555
A
K
103
D
K
K
1_555
A
DG
8
A
O6
DG
8
1_555
68.1
A
DG
2
A
O6
DG
2
1_555
A
K
103
D
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
108.4
A
DG
8
A
O6
DG
8
1_555
A
K
103
D
K
K
1_555
A
DG
14
A
O6
DG
14
1_555
70.0
A
DG
2
A
O6
DG
2
1_555
A
K
103
D
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
70.1
A
DG
8
A
O6
DG
8
1_555
A
K
103
D
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
107.3
A
DG
14
A
O6
DG
14
1_555
A
K
103
D
K
K
1_555
A
DG
20
A
O6
DG
20
1_555
70.7
A
DG
3
A
O6
DG
3
1_555
A
K
101
B
K
K
1_555
A
DG
4
A
O6
DG
4
1_555
72.7
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
65.5
A
DG
4
A
O6
DG
4
1_555
A
K
101
B
K
K
1_555
A
DG
9
A
O6
DG
9
1_555
90.7
A
DG
3
A
O6
DG
3
1_555
A
K
101
B
K
K
1_555
A
DG
10
A
O6
DG
10
1_555
125.5
A
DG
4
A
O6
DG
4
1_555
A
K
101
B
K
K
1_555
A
DG
10
A
O6
DG
10
1_555
75.6
A
DG
9
A
O6
DG
9
1_555
A
K
101
B
K
K
1_555
A
DG
10
A
O6
DG
10
1_555
71.9
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
102.7
A
DG
4
A
O6
DG
4
1_555
A
K
101
B
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
154.3
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
65.2
A
DG
10
A
O6
DG
10
1_555
A
K
101
B
K
K
1_555
A
DG
15
A
O6
DG
15
1_555
87.9
A
DG
3
A
O6
DG
3
1_555
A
K
101
B
K
K
1_555
A
DG
16
A
O6
DG
16
1_555
154.1
A
DG
4
A
O6
DG
4
1_555
A
K
101
B
K
K
1_555
A
DG
16
A
O6
DG
16
1_555
128.5
A
DG
9
A
O6
DG
9
1_555
A
K
101
B
K
K
1_555
A
DG
16
A
O6
DG
16
1_555
121.7
A
DG
10
A
O6
DG
10
1_555
A
K
101
B
K
K
1_555
A
DG
16
A
O6
DG
16
1_555
78.4
A
DG
15
A
O6
DG
15
1_555
A
K
101
B
K
K
1_555
A
DG
16
A
O6
DG
16
1_555
64.8
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
66.6
A
DG
4
A
O6
DG
4
1_555
A
K
101
B
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
128.1
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
100.1
A
DG
10
A
O6
DG
10
1_555
A
K
101
B
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
155.8
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
68.3
A
DG
16
A
O6
DG
16
1_555
A
K
101
B
K
K
1_555
A
DG
21
A
O6
DG
21
1_555
87.5
A
DG
3
A
O6
DG
3
1_555
A
K
101
B
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
92.5
A
DG
4
A
O6
DG
4
1_555
A
K
101
B
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
79.1
A
DG
9
A
O6
DG
9
1_555
A
K
101
B
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
157.8
A
DG
10
A
O6
DG
10
1_555
A
K
101
B
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
123.3
A
DG
15
A
O6
DG
15
1_555
A
K
101
B
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
126.6
A
DG
16
A
O6
DG
16
1_555
A
K
101
B
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
79.4
A
DG
21
A
O6
DG
21
1_555
A
K
101
B
K
K
1_555
A
DG
22
A
O6
DG
22
1_555
72.1
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
A
DA
1
A
DA
1
1
Y
1
15.89
1.20
119.70
135.59
A
A
A
C3'
O3'
P
DG
DG
DT
4
4
5
A
Y
1
-12.68
1.20
119.70
107.02
A
A
A
C3'
O3'
P
DG
DG
DT
4
4
5
B
Y
1
8.06
1.20
119.70
127.76
A
A
A
C3'
O3'
P
DT
DT
DT
11
11
12
Y
1
-6.55
1.00
110.10
103.55
A
A
A
C1'
O4'
C4'
DA
DA
DA
13
13
13
N
1
-9.96
1.20
119.70
109.74
A
A
A
C3'
O3'
P
DG
DG
DG
15
15
16
Y
40.963
-0.03
-0.01
0.00
-0.03
0.00
0.04
0.948
0.920
HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
0.27496
0.23123
0.23309
1.95
12.00
271
2807
5693
4.5
98.74
4.218
0.118
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.192
0.175
0.80
0.80
1.20
PDB ENTRY 3SC8
MAXIMUM LIKELIHOOD
MASK
1.95
12.00
51
561
63
447
0
0.007
0.012
593
2.008
1.512
911
0.079
0.200
66
0.013
0.020
271
0.407
0.423
1.999
23
361
20
100.00
1.84
22.36
3UYH
7126
2
0.06
1
21.00
10.5
99.6
0.8
1.84
1.88
2.9
1
10.7
100
data collection
CrysalisPro
Pro
phasing
PHASER
refinement
REFMAC
5.6.0117
data scaling
xia2
data reduction
xia2
data scaling
SCALA
Crystal structure of an intramolecular human telomeric DNA G-quadruplex bound by the naphthalene diimide compound, MM41
1
N
N
2
N
N
2
N
N
2
N
N
3
N
N
4
N
N
metalc
2.767
A
DG
2
A
O6
DG
2
1_555
A
K
102
C
K
K
1_555
metalc
2.891
A
DG
2
A
O6
DG
2
1_555
A
K
103
D
K
K
1_555
metalc
2.893
A
DG
3
A
O6
DG
3
1_555
A
K
101
B
K
K
1_555
metalc
2.728
A
DG
3
A
O6
DG
3
1_555
A
K
102
C
K
K
1_555
metalc
2.679
A
DG
4
A
O6
DG
4
1_555
A
K
101
B
K
K
1_555
metalc
2.784
A
DG
8
A
O6
DG
8
1_555
A
K
102
C
K
K
1_555
metalc
2.787
A
DG
8
A
O6
DG
8
1_555
A
K
103
D
K
K
1_555
metalc
2.961
A
DG
9
A
O6
DG
9
1_555
A
K
101
B
K
K
1_555
metalc
2.695
A
DG
9
A
O6
DG
9
1_555
A
K
102
C
K
K
1_555
metalc
2.640
A
DG
10
A
O6
DG
10
1_555
A
K
101
B
K
K
1_555
metalc
2.891
A
DG
14
A
O6
DG
14
1_555
A
K
102
C
K
K
1_555
metalc
2.750
A
DG
14
A
O6
DG
14
1_555
A
K
103
D
K
K
1_555
metalc
3.031
A
DG
15
A
O6
DG
15
1_555
A
K
101
B
K
K
1_555
metalc
2.889
A
DG
15
A
O6
DG
15
1_555
A
K
102
C
K
K
1_555
metalc
2.633
A
DG
16
A
O6
DG
16
1_555
A
K
101
B
K
K
1_555
metalc
2.817
A
DG
20
A
O6
DG
20
1_555
A
K
102
C
K
K
1_555
metalc
2.819
A
DG
20
A
O6
DG
20
1_555
A
K
103
D
K
K
1_555
metalc
2.953
A
DG
21
A
O6
DG
21
1_555
A
K
101
B
K
K
1_555
metalc
2.785
A
DG
21
A
O6
DG
21
1_555
A
K
102
C
K
K
1_555
metalc
2.635
A
DG
22
A
O6
DG
22
1_555
A
K
101
B
K
K
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
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
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
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
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
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
DNA
intramolecular, ligand-complex, G-quadruplex, telomere, DNA
3UYH
PDB
1
1
3UYH
AGGGTTAGGGTTAGGGTTAGGG
1
22
3UYH
1
22
3UYH
A
1
1
22
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 0DX A 104
A
0DX
104
Software
16
A
DG
3
A
DG
3
9
1_555
A
DG
4
A
DG
4
9
1_555
A
DG
9
A
DG
9
9
1_555
A
DG
10
A
DG
10
9
1_555
A
DG
15
A
DG
15
9
1_555
A
DG
16
A
DG
16
9
1_555
A
DG
21
A
DG
21
9
1_555
A
DG
22
A
DG
22
9
1_555
A
K
102
C
K
9
1_555
A
DG
2
A
DG
2
11
1_555
A
DG
3
A
DG
3
11
1_555
A
DG
8
A
DG
8
11
1_555
A
DG
9
A
DG
9
11
1_555
A
DG
14
A
DG
14
11
1_555
A
DG
15
A
DG
15
11
1_555
A
DG
20
A
DG
20
11
1_555
A
DG
21
A
DG
21
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
2
A
DG
2
10
4_555
A
DG
2
A
DG
2
10
1_555
A
DG
8
A
DG
8
10
1_555
A
DG
8
A
DG
8
10
4_555
A
DG
14
A
DG
14
10
4_555
A
DG
14
A
DG
14
10
1_555
A
DG
20
A
DG
20
10
1_555
A
DG
20
A
DG
20
10
4_555
A
K
102
C
K
10
1_555
A
K
102
C
K
10
4_555
A
DG
4
A
DG
4
16
1_555
A
DT
5
A
DT
5
16
1_555
A
DT
6
A
DT
6
16
3_544
A
DG
10
A
DG
10
16
1_555
A
DT
11
A
DT
11
16
1_555
A
DT
12
A
DT
12
16
5_544
A
DA
13
A
DA
13
16
5_544
A
DG
16
A
DG
16
16
1_555
A
DG
22
A
DG
22
16
1_555
A
HOH
217
F
HOH
16
1_555
A
HOH
219
F
HOH
16
1_555
A
HOH
220
F
HOH
16
1_555
A
HOH
227
F
HOH
16
1_555
A
HOH
229
F
HOH
16
1_555
A
HOH
242
F
HOH
16
1_555
A
HOH
251
F
HOH
16
1_555
152
P 31 2 1