0.035474
0.000000
0.000000
0.000000
0.035474
0.000000
0.000000
0.000000
0.018950
0.00000
0.00000
0.00000
Gallois, B.
Langlois D'Estaintot, B.
Brown, T.
Hunter, W.N.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
28.190
28.190
52.770
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
C26 H27 N O9
497.494
IDARUBICIN
4-DEMETHOXY-DAUNORUBICIN
non-polymer
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA linking
H2 O
18.015
WATER
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
Y
108
N
C
Y
109
N
C
Y
110
N
C
Y
111
N
C
Y
112
N
C
N
113
N
C
N
114
N
O
Y
115
N
C
Y
116
N
C
N
117
N
O
Y
118
N
C
N
119
S
C
N
120
N
O
N
121
N
C
N
122
S
C
N
123
N
O
N
124
N
C
N
125
N
O
N
126
N
C
N
127
N
C
Y
128
N
C
Y
129
N
C
N
130
N
O
Y
131
N
C
N
132
N
C
N
133
N
O
Y
134
N
C
N
135
R
C
N
136
N
C
N
137
S
C
N
138
N
N
N
139
S
C
N
140
N
O
N
141
S
C
N
142
N
O
N
143
N
C
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
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
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
O
N
172
N
P
N
173
N
O
N
174
N
O
N
175
N
O
N
176
N
C
N
177
R
C
N
178
N
O
N
179
S
C
N
180
N
O
N
181
N
C
N
182
R
C
N
183
N
N
N
184
N
C
N
185
N
O
N
186
N
N
N
187
N
C
N
188
N
O
N
189
N
C
N
190
N
C
N
191
N
C
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
O
N
208
N
H
N
209
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
Y
113
N
doub
Y
114
N
sing
N
115
N
sing
Y
116
N
sing
N
117
N
sing
Y
118
N
doub
N
119
N
sing
Y
120
N
sing
N
121
N
sing
N
122
N
sing
Y
123
N
doub
N
124
N
doub
N
125
N
sing
Y
126
N
doub
Y
127
N
sing
N
128
N
sing
Y
129
N
sing
N
130
N
sing
N
131
N
sing
Y
132
N
doub
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
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
doub
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
Y
152
N
sing
N
153
N
sing
Y
154
N
doub
N
155
N
sing
N
156
N
sing
N
157
N
doub
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
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
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
doub
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
doub
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
doub
N
210
N
sing
N
211
N
sing
N
212
N
doub
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
49
311
317
10.1107/S0907444992009983
15299520
The structure of an idarubicin-d(TGATCA) complex at high resolution.
1993
10.2210/pdb1d67/pdb
pdb_00001d67
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
DIFFRACTOMETER
RIGAKU AFC-5
x-ray
1
1.0
ROTATING ANODE
RIGAKU RU200
1808.229
DNA (5'-D(*TP*GP*AP*TP*CP*A)-3')
1
syn
polymer
497.494
IDARUBICIN
1
syn
non-polymer
18.015
water
35
nat
water
no
no
(DT)(DG)(DA)(DT)(DC)(DA)
TGATCA
A
polydeoxyribonucleotide
n
n
n
n
n
n
2.90
57.57
VAPOR DIFFUSION
6.50
pH 6.50, VAPOR DIFFUSION, temperature 295.00K
295.00
WATER
1
MPD
1
NA CACODYLATE
1
MG ACETATE
1
SPERMINE_HCL
1
WATER
2
MPD
2
8.992
1
20
A
1
A
6
1.140
A_DT1:DA6_A
1
0.503
-0.087
-0.039
-0.191
-15.554
1
19
A
2
A
5
-1.459
A_DG2:DC5_A
2
-0.088
-0.113
-0.418
-0.158
-10.942
1
20
A
3
A
4
2.551
A_DA3:DT4_A
3
-2.536
0.068
-0.034
-0.168
10.942
1
20
A
4
A
3
2.551
A_DT4:DA3_A
4
-2.536
-0.068
-0.034
-0.168
15.554
1
19
A
5
A
2
-1.459
A_DC5:DG2_A
5
-0.088
0.113
-0.418
-0.158
-8.992
1
20
A
6
A
1
1.140
A_DA6:DT1_A
6
0.503
0.087
-0.039
-0.191
7.080
35.490
A
A
1
2
-0.544
A
A
6
5
7.032
-0.331
1.012
1.137
AA_DT1DG2:DC5DA6_AA
1
2.954
-4.852
35.369
1.969
-0.727
3.460
31.439
A
A
2
3
-0.358
A
A
5
4
3.277
-0.193
-1.280
0.663
AA_DG2DA3:DT4DC5_AA
2
-6.290
11.683
30.818
1.260
1.137
2.827
32.663
A
A
3
4
5.709
A
A
4
3
2.887
3.206
0.000
-0.487
AA_DA3DT4:DA3DT4_AA
3
0.000
0.000
32.510
-1.352
0.000
3.460
31.439
A
A
4
5
-0.358
A
A
3
2
3.277
-0.193
1.280
0.663
AA_DT4DC5:DG2DA3_AA
4
6.290
-11.683
30.818
1.260
-1.137
7.080
35.490
A
A
5
6
-0.544
A
A
2
1
7.032
-0.331
-1.012
1.137
AA_DC5DA6:DT1DG2_AA
5
-2.954
4.852
35.369
1.969
0.727
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
1993-07-15
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
1992-03-31
REL
REL
DM5
IDARUBICIN
HOH
water
DM5
7
2
DM5
DM5
7
A
HOH
8
3
HOH
HOH
8
A
HOH
9
3
HOH
HOH
9
A
HOH
10
3
HOH
HOH
10
A
HOH
11
3
HOH
HOH
11
A
HOH
12
3
HOH
HOH
12
A
HOH
13
3
HOH
HOH
13
A
HOH
14
3
HOH
HOH
14
A
HOH
15
3
HOH
HOH
15
A
HOH
16
3
HOH
HOH
16
A
HOH
17
3
HOH
HOH
17
A
HOH
18
3
HOH
HOH
18
A
HOH
19
3
HOH
HOH
19
A
HOH
20
3
HOH
HOH
20
A
HOH
21
3
HOH
HOH
21
A
HOH
22
3
HOH
HOH
22
A
HOH
23
3
HOH
HOH
23
A
HOH
24
3
HOH
HOH
24
A
HOH
25
3
HOH
HOH
25
A
HOH
26
3
HOH
HOH
26
A
HOH
27
3
HOH
HOH
27
A
HOH
28
3
HOH
HOH
28
A
HOH
29
3
HOH
HOH
29
A
HOH
30
3
HOH
HOH
30
A
HOH
31
3
HOH
HOH
31
A
HOH
32
3
HOH
HOH
32
A
HOH
33
3
HOH
HOH
33
A
HOH
34
3
HOH
HOH
34
A
HOH
35
3
HOH
HOH
35
A
HOH
36
3
HOH
HOH
36
A
HOH
37
3
HOH
HOH
37
A
HOH
38
3
HOH
HOH
38
A
HOH
39
3
HOH
HOH
39
A
HOH
40
3
HOH
HOH
40
A
HOH
41
3
HOH
HOH
41
A
HOH
42
3
HOH
HOH
42
A
T
1
n
1
DT
1
A
G
2
n
2
DG
2
A
A
3
n
3
DA
3
A
T
4
n
4
DT
4
A
C
5
n
5
DC
5
A
A
6
n
6
DA
6
A
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
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
8_555
-y,-x,-z+1/2
crystal symmetry operation
0.0000000000
0.0000000000
26.3850000000
1
-5.05
0.80
109.40
104.35
A
A
A
O5'
C5'
C4'
DT
DT
DT
1
1
1
N
1
-4.53
0.60
127.20
122.67
A
A
A
C2
N3
C4
DT
DT
DT
1
1
1
N
1
3.76
0.60
115.20
118.96
A
A
A
N3
C4
C5
DT
DT
DT
1
1
1
N
1
-5.07
0.80
102.40
97.33
A
A
A
C3'
C2'
C1'
DG
DG
DG
2
2
2
N
1
5.59
0.30
108.30
113.89
A
A
A
O4'
C1'
N9
DG
DG
DG
2
2
2
N
1
-8.25
0.80
109.40
101.15
A
A
A
O5'
C5'
C4'
DA
DA
DA
3
3
3
N
1
-5.30
0.80
105.90
100.60
A
A
A
O4'
C1'
C2'
DT
DT
DT
4
4
4
N
1
-6.09
0.70
108.00
101.91
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
-8.74
0.80
109.40
100.66
A
A
A
O5'
C5'
C4'
DC
DC
DC
5
5
5
N
1
18.12
0.30
108.30
126.42
A
A
A
O4'
C1'
N1
DC
DC
DC
5
5
5
N
1
-3.38
0.50
117.70
114.32
A
A
A
C5
C6
N1
DA
DA
DA
6
6
6
N
1
A
A
C6
N1
DG
DG
2
2
-0.056
0.007
1.391
1.335
N
1
A
A
O4'
C1'
DT
DT
4
4
0.090
0.011
1.420
1.510
N
1
A
A
O4'
C4'
DT
DT
4
4
-0.074
0.010
1.446
1.372
N
1
A
A
C6
N1
DA
DA
6
6
0.080
0.007
1.351
1.431
N
0.2220000
1.600
8.000
2032
1
3.000
TR
isotropic
TR
isotropic
1.600
8.000
35
191
36
120
0
0.020
0.030
fix
fix
1.500
1D67
4578
1
refinement
NUCLSQ
THE MOLECULAR STRUCTURE OF AN IDARUBICIN-D(TGATCA) COMPLEX AT HIGH RESOLUTION
1
N
N
2
N
N
3
N
N
hydrog
WATSON-CRICK
A
DT
1
A
N3
DT
1
1_555
A
DA
6
A
N1
DA
6
8_555
hydrog
WATSON-CRICK
A
DT
1
A
O4
DT
1
1_555
A
DA
6
A
N6
DA
6
8_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
A
DC
5
A
N3
DC
5
8_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
A
DC
5
A
O2
DC
5
8_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
A
DC
5
A
N4
DC
5
8_555
hydrog
WATSON-CRICK
A
DA
3
A
N1
DA
3
1_555
A
DT
4
A
N3
DT
4
8_555
hydrog
WATSON-CRICK
A
DA
3
A
N6
DA
3
1_555
A
DT
4
A
O4
DT
4
8_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
A
DA
3
A
N1
DA
3
8_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
A
DA
3
A
N6
DA
3
8_555
hydrog
WATSON-CRICK
A
DC
5
A
N3
DC
5
1_555
A
DG
2
A
N1
DG
2
8_555
hydrog
WATSON-CRICK
A
DC
5
A
N4
DC
5
1_555
A
DG
2
A
O6
DG
2
8_555
hydrog
WATSON-CRICK
A
DC
5
A
O2
DC
5
1_555
A
DG
2
A
N2
DG
2
8_555
hydrog
WATSON-CRICK
A
DA
6
A
N1
DA
6
1_555
A
DT
1
A
N3
DT
1
8_555
hydrog
WATSON-CRICK
A
DA
6
A
N6
DA
6
1_555
A
DT
1
A
O4
DT
1
8_555
DNA
RIGHT HANDED DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DNA
1D67
PDB
1
1D67
1
6
1D67
1
6
1D67
A
1
1
6
BINDING SITE FOR RESIDUE DM5 A 7
A
DM5
7
Software
10
A
DT
1
A
DT
1
10
8_555
A
DG
2
A
DG
2
10
8_555
A
DA
3
A
DA
3
10
8_555
A
DT
4
A
DT
4
10
1_555
A
DC
5
A
DC
5
10
1_555
A
DA
6
A
DA
6
10
1_555
A
HOH
17
C
HOH
10
1_555
A
HOH
18
C
HOH
10
1_555
A
HOH
33
C
HOH
10
1_555
A
HOH
42
C
HOH
10
8_555
92
P 41 21 2