1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Robinson, H.
Wang, A.H.-J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C62 H66 N2 O20 2
1159.189
4-METHYLBENZYL-N-BIS[DAUNOMYCIN]
WP631
non-polymer
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
US
Biochemistry
BICHAW
0033
0006-2960
36
8663
8670
10.1021/bi970842j
9289011
Binding of two novel bisdaunorubicins to DNA studied by NMR spectroscopy.
1997
10.2210/pdb1al9/pdb
pdb_00001al9
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
WP631 IS AN INTERCALATOR
2426.617
DNA (5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3')
2
syn
polymer
1159.189
4-METHYLBENZYL-N-BIS[DAUNOMYCIN]
1
syn
non-polymer
no
no
(DA)(DC)(DG)(DT)(DA)(DC)(DG)(DT)
ACGTACGT
A,B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
5.149
1
20
A
1
B
16
8.773
A_DA1:DT16_B
1
3.767
0.255
0.453
-0.022
13.971
1
19
A
2
B
15
-6.375
A_DC2:DG15_B
2
-6.261
0.587
-0.035
-0.276
-18.129
1
19
A
3
B
14
4.370
A_DG3:DC14_B
3
9.481
-0.482
-0.324
-0.124
-6.360
1
20
A
4
B
13
-1.813
A_DT4:DA13_B
4
-11.052
-0.083
0.312
-0.067
6.429
1
20
A
5
B
12
-1.893
A_DA5:DT12_B
5
-11.165
0.086
0.320
-0.074
18.184
1
19
A
6
B
11
4.374
A_DC6:DG11_B
6
9.451
0.483
-0.322
-0.133
-13.983
1
19
A
7
B
10
-6.295
A_DG7:DC10_B
7
-6.332
-0.600
-0.033
-0.286
-5.284
1
20
A
8
B
9
8.955
A_DT8:DA9_B
8
3.881
-0.268
0.459
-0.021
3.031
30.909
A
A
1
2
-10.749
B
B
16
15
3.105
-5.668
-0.191
-0.320
AA_DA1DC2:DG15DT16_BB
1
5.499
-10.428
29.907
0.448
1.375
6.862
35.666
A
A
2
3
-7.724
B
B
15
14
6.947
-4.715
1.037
0.611
AA_DC2DG3:DC14DG15_BB
2
2.263
-3.707
35.292
2.448
-0.997
3.105
27.991
A
A
3
4
-2.390
B
B
14
13
2.980
-1.150
-0.910
-0.367
AA_DG3DT4:DA13DC14_BB
3
-4.904
10.191
27.543
-0.504
0.792
3.600
35.924
A
A
4
5
16.783
B
B
13
12
3.464
10.217
-0.002
0.979
AA_DT4DA5:DT12DA13_BB
4
-0.103
0.170
34.487
-0.024
-0.013
3.107
28.023
A
A
5
6
-2.508
B
B
12
11
2.981
-1.208
0.911
-0.368
AA_DA5DC6:DG11DT12_BB
5
4.985
-10.351
27.558
-0.492
-0.775
6.863
35.692
A
A
6
7
-7.730
B
B
11
10
6.948
-4.722
-1.036
0.611
AA_DC6DG7:DC10DG11_BB
6
-2.267
3.711
35.318
2.448
0.994
3.031
30.966
A
A
7
8
-10.588
B
B
10
9
3.106
-5.593
0.191
-0.320
AA_DG7DT8:DA9DC10_BB
7
-5.586
10.574
29.964
0.431
-1.388
database_2
pdbx_database_status
pdbx_struct_assembly
pdbx_struct_oper_list
struct_site
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
1
0
1997-09-17
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
MINIMIZED AVERAGE STRUCTURE
Y
BNL
1997-06-12
REL
REL
BDA
4-METHYLBENZYL-N-BIS[DAUNOMYCIN]
IONIC_STRENGTH: 20 MM PRESSURE: NULL SOLVENT SYSTEM: H2O
MINIMIZED AVERAGE
1
1
NOESY
TOCSY
7.0
275
K
REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NOE-RMD
BRUNGER
refinement
X-PLOR
structure solution
X-PLOR
structure solution
SPEDREF
750
Varian
INOVA 750
DM1
17
2
BDA
BDA
17
A
A
1
n
1
DA
1
A
C
2
n
2
DC
2
A
G
3
n
3
DG
3
A
T
4
n
4
DT
4
A
A
5
n
5
DA
5
A
C
6
n
6
DC
6
A
G
7
n
7
DG
7
A
T
8
n
8
DT
8
A
A
9
n
1
DA
9
B
C
10
n
2
DC
10
B
G
11
n
3
DG
11
B
T
12
n
4
DT
12
B
A
13
n
5
DA
13
B
C
14
n
6
DC
14
B
G
15
n
7
DG
15
B
T
16
n
8
DT
16
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
A
DT
4
0.085
SIDE CHAIN
1
A
DC
6
0.092
SIDE CHAIN
1
B
DT
12
0.085
SIDE CHAIN
1
B
DC
14
0.092
SIDE CHAIN
1
4.48
0.60
106.00
110.48
A
A
A
O4'
C4'
C3'
DA
DA
DA
1
1
1
N
1
-5.02
0.70
108.00
102.98
A
A
A
O4'
C1'
N9
DA
DA
DA
1
1
1
N
1
-5.15
0.80
105.90
100.75
A
A
A
O4'
C1'
C2'
DC
DC
DC
2
2
2
N
1
4.80
0.30
108.30
113.10
A
A
A
O4'
C1'
N1
DC
DC
DC
2
2
2
N
1
3.63
0.60
106.00
109.63
A
A
A
O4'
C4'
C3'
DG
DG
DG
3
3
3
N
1
-2.51
0.40
106.40
103.89
A
A
A
C8
N9
C4
DG
DG
DG
3
3
3
N
1
4.34
0.30
108.30
112.64
A
A
A
O4'
C1'
N1
DT
DT
DT
4
4
4
N
1
-4.37
0.70
102.20
97.83
A
A
A
C4'
C3'
C2'
DA
DA
DA
5
5
5
N
1
2.29
0.30
108.30
110.59
A
A
A
O4'
C1'
N9
DA
DA
DA
5
5
5
N
1
2.63
0.30
108.30
110.93
A
A
A
O4'
C1'
N1
DC
DC
DC
6
6
6
N
1
5.26
0.60
106.00
111.26
A
A
A
O4'
C4'
C3'
DG
DG
DG
7
7
7
N
1
-5.25
0.60
122.90
117.65
A
A
A
C6
C5
C7
DT
DT
DT
8
8
8
N
1
4.52
0.60
106.00
110.52
B
B
B
O4'
C4'
C3'
DA
DA
DA
9
9
9
N
1
-4.95
0.70
108.00
103.05
B
B
B
O4'
C1'
N9
DA
DA
DA
9
9
9
N
1
-5.14
0.80
105.90
100.76
B
B
B
O4'
C1'
C2'
DC
DC
DC
10
10
10
N
1
4.85
0.30
108.30
113.15
B
B
B
O4'
C1'
N1
DC
DC
DC
10
10
10
N
1
3.72
0.60
106.00
109.72
B
B
B
O4'
C4'
C3'
DG
DG
DG
11
11
11
N
1
-2.48
0.40
106.40
103.92
B
B
B
C8
N9
C4
DG
DG
DG
11
11
11
N
1
4.09
0.30
108.30
112.39
B
B
B
O4'
C1'
N1
DT
DT
DT
12
12
12
N
1
-4.44
0.70
102.20
97.76
B
B
B
C4'
C3'
C2'
DA
DA
DA
13
13
13
N
1
2.31
0.30
108.30
110.61
B
B
B
O4'
C1'
N9
DA
DA
DA
13
13
13
N
1
2.62
0.30
108.30
110.92
B
B
B
O4'
C1'
N1
DC
DC
DC
14
14
14
N
1
4.85
0.60
106.00
110.85
B
B
B
O4'
C4'
C3'
DG
DG
DG
15
15
15
N
1
-3.79
0.60
122.90
119.11
B
B
B
C6
C5
C7
DT
DT
DT
16
16
16
N
1
B
B
C5
C7
DT
DT
12
12
0.037
0.006
1.496
1.533
N
model building
X-PLOR
refinement
X-PLOR
phasing
X-PLOR
NMR STUDY OF DNA (5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3') SELF-COMPLEMENTARY DUPLEX COMPLEXED WITH A BIS-DAUNORUBICIN, MINIMIZED AVERAGE STRUCTURE
1
N
N
1
N
N
2
N
N
hydrog
WATSON-CRICK
A
DA
1
A
N1
DA
1
1_555
B
DT
16
B
N3
DT
8
1_555
hydrog
WATSON-CRICK
A
DA
1
A
N6
DA
1
1_555
B
DT
16
B
O4
DT
8
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N3
DC
2
1_555
B
DG
15
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
2
A
N4
DC
2
1_555
B
DG
15
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
A
DC
2
A
O2
DC
2
1_555
B
DG
15
B
N2
DG
7
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N1
DG
3
1_555
B
DC
14
B
N3
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
3
A
N2
DG
3
1_555
B
DC
14
B
O2
DC
6
1_555
hydrog
WATSON-CRICK
A
DG
3
A
O6
DG
3
1_555
B
DC
14
B
N4
DC
6
1_555
hydrog
WATSON-CRICK
A
DT
4
A
N3
DT
4
1_555
B
DA
13
B
N1
DA
5
1_555
hydrog
WATSON-CRICK
A
DT
4
A
O4
DT
4
1_555
B
DA
13
B
N6
DA
5
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N1
DA
5
1_555
B
DT
12
B
N3
DT
4
1_555
hydrog
WATSON-CRICK
A
DA
5
A
N6
DA
5
1_555
B
DT
12
B
O4
DT
4
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N3
DC
6
1_555
B
DG
11
B
N1
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
6
A
N4
DC
6
1_555
B
DG
11
B
O6
DG
3
1_555
hydrog
WATSON-CRICK
A
DC
6
A
O2
DC
6
1_555
B
DG
11
B
N2
DG
3
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N1
DG
7
1_555
B
DC
10
B
N3
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
7
A
N2
DG
7
1_555
B
DC
10
B
O2
DC
2
1_555
hydrog
WATSON-CRICK
A
DG
7
A
O6
DG
7
1_555
B
DC
10
B
N4
DC
2
1_555
hydrog
WATSON-CRICK
A
DT
8
A
N3
DT
8
1_555
B
DA
9
B
N1
DA
1
1_555
hydrog
WATSON-CRICK
A
DT
8
A
O4
DT
8
1_555
B
DA
9
B
N6
DA
1
1_555
DNA
COMPLEX (DEOXYRIBONUCLEIC ACID-DRUG), BIS-INTERCALATOR, DAUNORUBICIN, DNA, DEOXYRIBONUCLEIC ACID
1AL9
PDB
1
1AL9
1
8
1AL9
1
8
1AL9
A
1
1
8
9
16
1AL9
9
16
1AL9
B
1
1
8
BINDING SITE FOR RESIDUE BDA A 17
A
BDA
17
Software
12
A
DC
2
A
DC
2
12
1_555
A
DG
3
A
DG
3
12
1_555
A
DT
4
A
DT
4
12
1_555
A
DA
5
A
DA
5
12
1_555
A
DC
6
A
DC
6
12
1_555
A
DG
7
A
DG
7
12
1_555
B
DC
10
B
DC
2
12
1_555
B
DG
11
B
DG
3
12
1_555
B
DT
12
B
DT
4
12
1_555
B
DA
13
B
DA
5
12
1_555
B
DC
14
B
DC
6
12
1_555
B
DG
15
B
DG
7
12
1_555
1
P 1