1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Thiviyanathan, V.
Vyazovkina, K.V.
Gozansky, E.K.
Bichenkova, E.
Abramova, T.V.
Luxon, B.A.
Lebedev, A.V.
Gorenstein, D.G.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C10 H16 N3 O6 P
305.224
n
2'-DEOXY-CYTIDINE-5'-RP-MONOMETHYLPHOSPHONATE
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
C11 H16 N5 O5 P
329.249
n
2'-DEOXY-ADENOSINE-5'-RP-MONOMETHYLPHOSPHONATE
DNA linking
N
1
S
P
N
2
N
C
N
3
N
O
N
4
N
O
N
5
N
C
N
6
R
C
N
7
N
O
N
8
R
C
N
9
N
N
N
10
N
C
N
11
N
C
N
12
N
C
N
13
N
N
N
14
N
N
N
15
N
C
N
16
N
O
N
17
S
C
N
18
N
C
N
19
N
O
N
20
N
O
N
21
N
H
N
22
N
H
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
S
P
N
145
N
C
N
146
N
O
N
147
N
O
N
148
N
C
N
149
R
C
N
150
N
O
N
151
R
C
Y
152
N
N
Y
153
N
C
Y
154
N
N
Y
155
N
C
Y
156
N
C
N
157
N
N
Y
158
N
N
Y
159
N
C
Y
160
N
N
Y
161
N
C
N
162
S
C
N
163
N
C
N
164
N
O
N
165
N
O
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
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
1
N
sing
N
2
N
doub
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
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
doub
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
doub
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
doub
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
doub
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
doub
N
64
N
sing
N
65
N
doub
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
doub
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
doub
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
Y
96
N
sing
Y
97
N
sing
Y
98
N
doub
N
99
N
sing
Y
100
N
sing
N
101
N
sing
Y
102
N
doub
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
doub
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
sing
N
135
N
sing
N
136
N
sing
N
137
N
doub
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
doub
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
doub
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
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
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
Y
167
N
sing
Y
168
N
sing
Y
169
N
doub
N
170
N
sing
Y
171
N
sing
Y
172
N
doub
Y
173
N
sing
N
174
N
sing
Y
175
N
sing
N
176
N
sing
N
177
N
sing
Y
178
N
doub
Y
179
N
sing
N
180
N
sing
Y
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
US
Biochemistry
BICHAW
0033
0006-2960
41
827
838
10.1021/bi011551k
11790104
Structure of hybrid backbone methylphosphonate DNA heteroduplexes: effect of R and S stereochemistry.
2002
10.2210/pdb1k1r/pdb
pdb_00001k1r
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
SINGLE WAVELENGTH
M
1
1.0
2448.613
5'-D(*TP*GP*TP*TP*TP*GP*GP*C)-3'
1
syn
polymer
2063.577
5'-D(*CP*(CMR)P*(RMP)P*(RMP)P*(RMP)P*(CMR)P*(RMP))-3'
1
syn
polymer
no
no
(DT)(DG)(DT)(DT)(DT)(DG)(DG)(DC)
TGTTTGGC
A
polydeoxyribonucleotide
no
yes
(DC)(CMR)(RMP)(RMP)(RMP)(CMR)(RMP)
CCAAACA
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
15.133
1
20
A
1
B
15
-0.202
A_DT1:RMP15_B
1
-26.104
-0.100
-0.504
-0.073
-8.314
1
19
A
2
B
14
-1.850
A_DG2:CMR14_B
2
-21.540
-0.208
-0.063
-0.243
-20.532
1
20
A
3
B
13
1.382
A_DT3:RMP13_B
3
-18.306
0.110
-0.309
-0.215
-28.320
1
20
A
4
B
12
2.673
A_DT4:RMP12_B
4
-21.719
0.083
-0.168
-0.157
-20.246
1
20
A
5
B
11
0.738
A_DT5:RMP11_B
5
-10.334
-0.108
0.025
-0.088
-19.590
1
19
A
6
B
10
-5.610
A_DG6:CMR10_B
6
0.604
0.107
-0.377
-0.066
-2.709
1
19
A
7
B
9
-5.570
A_DG7:DC9_B
7
11.041
0.436
-0.111
-0.139
3.860
42.049
A
A
1
2
15.043
B
B
15
14
4.176
10.597
-0.686
-0.983
AA_DT1DG2:CMR14RMP15_BB
1
-9.580
13.598
39.652
-2.762
-0.302
3.534
35.181
A
A
2
3
-0.619
B
B
14
13
3.557
-0.374
-0.470
-0.190
AA_DG2DT3:RMP13CMR14_BB
2
1.600
-2.648
35.144
-0.255
1.035
3.546
44.002
A
A
3
4
20.125
B
B
13
12
3.606
14.809
0.283
0.445
AA_DT3DT4:RMP12RMP13_BB
3
-1.475
2.004
41.527
-0.984
-0.535
3.118
32.107
A
A
4
5
6.139
B
B
12
11
3.207
3.373
0.510
0.582
AA_DT4DT5:RMP11RMP12_BB
4
-5.558
10.116
31.459
0.462
-1.896
2.986
29.126
A
A
5
6
13.142
B
B
11
10
3.338
6.522
-0.124
-0.908
AA_DT5DG6:CMR10RMP11_BB
5
5.067
-10.211
27.955
-3.213
1.341
3.175
30.601
A
A
6
7
-5.086
B
B
10
9
3.063
-2.681
0.760
-1.394
AA_DG6DG7:DC9CMR10_BB
6
0.157
-0.297
30.485
-2.134
-1.411
database_2
pdbx_nmr_exptl_sample_conditions
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Experimental preparation
Data collection
1
0
2002-06-19
1
1
2008-04-27
1
2
2011-07-13
1
3
2022-02-23
1
4
2024-05-22
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_exptl_sample_conditions.pressure_units
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE / DNA DUPLEX
Chiral center at the fifth position of chain B is changed to S.
RCSB
Y
RCSB
2001-09-25
REL
1
2D NOESY
DQF-COSY
100 mM
7.0
1
atm
298
K
molecular dynamics matrix relaxation
100 mM NaCl, 10 mM Phosphate, 0.1 mM EDTA
H2O, D2O
varian
data analysis
VNMR
5.1
UCSF
refinement
Amber
5.0
Post, Meadows, Gorenstein
iterative matrix relaxation
MORASS
2.0
750
Varian
UNITYPLUS
600
Varian
UNITYPLUS
400
Varian
UNITYPLUS
T
1
n
1
DT
1
A
G
2
n
2
DG
2
A
T
3
n
3
DT
3
A
T
4
n
4
DT
4
A
T
5
n
5
DT
5
A
G
6
n
6
DG
6
A
G
7
n
7
DG
7
A
C
8
n
8
DC
8
A
C
9
n
1
DC
9
B
CMR
10
n
2
CMR
10
B
RMP
11
n
3
RMP
11
B
RMP
12
n
4
RMP
12
B
RMP
13
n
5
RMP
13
B
CMR
14
n
6
CMR
14
B
RMP
15
n
7
RMP
15
B
author_defined_assembly
2
dimeric
B
CMR
10
B
CMR
2
DC
B
RMP
11
B
RMP
3
DA
B
RMP
12
B
RMP
4
DA
B
RMP
13
B
RMP
5
DA
B
CMR
14
B
CMR
6
DC
B
RMP
15
B
RMP
7
DA
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
DG
7
0.092
SIDE CHAIN
1
3.65
0.30
108.30
111.95
A
A
A
O4'
C1'
N1
DT
DT
DT
1
1
1
N
1
1.98
0.30
108.30
110.28
A
A
A
O4'
C1'
N1
DT
DT
DT
3
3
3
N
1
2.92
0.30
108.30
111.22
A
A
A
O4'
C1'
N1
DT
DT
DT
5
5
5
N
1
-4.27
0.60
122.90
118.63
A
A
A
C6
C5
C7
DT
DT
DT
5
5
5
N
1
4.21
0.30
108.30
112.51
A
A
A
O4'
C1'
N9
DG
DG
DG
6
6
6
N
1
2.06
0.30
108.30
110.36
A
A
A
O4'
C1'
N9
DG
DG
DG
7
7
7
N
1
-4.38
0.70
121.90
117.52
A
A
A
N3
C2
O2
DC
DC
DC
8
8
8
N
HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE/DNA DUPLEX
1
N
N
2
N
N
covale
1.616
both
B
DC
9
B
O3'
DC
1
1_555
B
CMR
10
B
P
CMR
2
1_555
covale
1.623
both
B
CMR
10
B
O3'
CMR
2
1_555
B
RMP
11
B
P
RMP
3
1_555
covale
1.611
both
B
RMP
11
B
O3'
RMP
3
1_555
B
RMP
12
B
P
RMP
4
1_555
covale
1.617
both
B
RMP
12
B
O3'
RMP
4
1_555
B
RMP
13
B
P
RMP
5
1_555
covale
1.622
both
B
RMP
13
B
O3'
RMP
5
1_555
B
CMR
14
B
P
CMR
6
1_555
covale
1.626
both
B
CMR
14
B
O3'
CMR
6
1_555
B
RMP
15
B
P
RMP
7
1_555
hydrog
WATSON-CRICK
A
DT
1
A
N3
DT
1
1_555
B
RMP
15
B
N1
RMP
7
1_555
hydrog
WATSON-CRICK
A
DT
1
A
O4
DT
1
1_555
B
RMP
15
B
N6
RMP
7
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N1
DG
2
1_555
B
CMR
14
B
N3
CMR
6
1_555
hydrog
WATSON-CRICK
A
DG
2
A
N2
DG
2
1_555
B
CMR
14
B
O2
CMR
6
1_555
hydrog
WATSON-CRICK
A
DG
2
A
O6
DG
2
1_555
B
CMR
14
B
N4
CMR
6
1_555
hydrog
WATSON-CRICK
A
DT
3
A
N3
DT
3
1_555
B
RMP
13
B
N1
RMP
5
1_555
hydrog
WATSON-CRICK
A
DT
3
A
O4
DT
3
1_555
B
RMP
13
B
N6
RMP
5
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
B
RMP
12
B
N1
RMP
4
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
B
RMP
12
B
N6
RMP
4
1_555
hydrog
WATSON-CRICK
A
DT
5
A
N3
DT
5
1_555
B
RMP
11
B
N1
RMP
3
1_555
hydrog
WATSON-CRICK
A
DT
5
A
O4
DT
5
1_555
B
RMP
11
B
N6
RMP
3
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N1
DG
6
1_555
B
CMR
10
B
N3
CMR
2
1_555
hydrog
WATSON-CRICK
A
DG
6
A
N2
DG
6
1_555
B
CMR
10
B
O2
CMR
2
1_555
hydrog
WATSON-CRICK
A
DG
6
A
O6
DG
6
1_555
B
CMR
10
B
N4
CMR
2
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
B
DC
9
B
N3
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
B
DC
9
B
O2
DC
1
1_555
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
B
DC
9
B
N4
DC
1
1_555
DNA
methyl phosphonate, modified DNA, anti sense, aptamers, DNA
1K1R
PDB
1
1K1R
1K1R
PDB
2
1K1R
1
8
1K1R
1
8
1K1R
A
1
1
8
9
15
1K1R
9
15
1K1R
B
2
1
7