Chemical Components in the PDB

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BSJ : Summary

Code

BSJ

One-letter code

X

Molecule name

(3R,9Z)-17-[(2R,3S,4R,5R,6R)-5-amino-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl]oxy}-3,4-dihydroxytetrahydro-2H-pyran-2-yl]-3-hydroxy-2,2-dimethyl-4,8,15-trioxo-12-thia-5,9,16-triazaheptadec-9-en-1-yl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate

Systematic names

ProgramVersionName
ACDLabs 10.04 (3R,9Z)-17-[(2R,3S,4R,5R,6R)-5-amino-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl]oxy}-3,4-dihydroxytetrahydro-2H-pyran-2-yl]-3-hydroxy-2,2-dimethyl-4,8,15-trioxo-12-thia-5,9,16-triazaheptadec-9-en-1-yl [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
OpenEye OEToolkits 1.5.0 [(3R)-4-[[3-[2-[3-[[(2R,3S,4R,5R,6R)-5-amino-6-[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxy-cyclohexyl]oxy-3,4-dihydroxy-oxan-2-yl]methylamino]-3-oxo-propyl]sulfanylethylideneamino]-3-oxo-propyl]amino]-3-hydroxy-2,2-dimethyl-4-oxo-butyl] [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] hydrogen phosphate

Formula

C36 H62 N11 O23 P3 S

Formal charge

0

Molecular weight

1141.924 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OC1C(O)C(OC1COP(=O)(O)OP(=O)(O)OCC(C)(C)C(O)C(=O)NCCC(=O)\N=C/CSCCC(=O)NCC3OC(OC2C(O)C(O)C(N)CC2N)C(N)C(O)C3O)n4c5ncnc(N)c5nc4
SMILES CACTVS 3.341 CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)N=CCSCCC(=O)NC[CH]4O[CH](O[CH]5[CH](N)C[CH](N)[CH](O)[CH]5O)[CH](N)[CH](O)[CH]4O
SMILES OpenEye OEToolkits 1.5.0 CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)N=CCSCCC(=O)NCC4C(C(C(C(O4)OC5C(CC(C(C5O)O)N)N)N)O)O)O
Canonical SMILES CACTVS 3.341 CC(C)(CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)N=CCSCCC(=O)NC[C@H]4O[C@H](O[C@@H]5[C@@H](N)C[C@@H](N)[C@H](O)[C@H]5O)[C@H](N)[C@@H](O)[C@@H]4O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(C)(CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)/N=C\CSCCC(=O)NC[C@@H]4[C@H]([C@@H]([C@H]([C@H](O4)O[C@@H]5[C@H](C[C@H]([C@@H]([C@H]5O)O)N)N)N)O)O)O

IUPAC InChI

InChI=1S/C36H62N11O23P3S/c1-36(2,12-65-73(62,63)70-72(60,61)64-11-18-29(69-71(57,58)59)27(54)34(66-18)47-14-46-22-31(40)44-13-45-32(22)47)30(55)33(56)42-5-3-19(48)41-6-8-74-7-4-20(49)43-10-17-24(51)25(52)21(39)35(67-17)68-28-16(38)9-15(37)23(50)26(28)53/h6,13-18,21,23-30,34-35,50-55H,3-5,7-12,37-39H2,1-2H3,(H,42,56)(H,43,49)(H,60,61)(H,62,63)(H2,40,44,45)(H2,57,58,59)/b41-6-/t15-,16+,17-,18-,21-,23+,24-,25-,26-,27-,28-,29-,30+,34-,35-/m1/s1

IUPAC InChI key

HXXBCMJRHXNFMC-BOUWNZBBSA-N
BSJ

wwPDB Information

Atom count

136 (74 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

Is modified

No

Standard parent

Not Assigned

Defined at

2007-09-14

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



BSJ : Atoms of Molecule

Total Number of Atoms: 136
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O56 O O56 N N N 0 9.482 -1.215 16.52
2 C66 C C66 R N N 0 10.749 -0.799 16.022
3 C65 C C65 S N N 0 10.591 -0.306 14.57
4 O55 O O55 N N N 0 9.612 0.757 14.474
5 C64 C C64 R N N 0 11.949 0.101 13.951
6 N53 N N53 N N N 0 11.775 0.419 12.511
7 C63 C C63 N N N 0 13.009 -1.018 14.092
8 C62 C C62 S N N 0 13.093 -1.567 15.543
9 N52 N N52 N N N 0 14.082 -2.663 15.663
10 C61 C C61 R N N 0 11.728 -2.01 16.108
11 O54 O O54 N N N 0 12.031 -2.359 17.471
12 C60 C C60 R N N 0 11.055 -3.188 18.154
13 O53 O O53 N N N 0 10.873 -4.462 17.467
14 C55 C C55 R N N 0 11.49 -3.396 19.613
15 N50 N N50 N N N 0 11.775 -2.083 20.245
16 C56 C C56 R N N 0 12.702 -4.346 19.669
17 O51 O O51 N N N 0 13.111 -4.608 21.017
18 C57 C C57 S N N 0 12.358 -5.656 18.93
19 O52 O O52 N N N 0 13.465 -6.542 18.951
20 C59 C C59 R N N 0 12.061 -5.284 17.46
21 C58 C C58 N N N 0 11.892 -6.419 16.439
22 N51 N N51 N N N 0 10.827 -7.339 16.858
23 C54 C C54 N N N 0 10.53 -8.433 16.138
24 O57 O O57 N N N 0 11.113 -8.761 15.093
25 C53 C C53 N N N 0 9.405 -9.305 16.741
26 C52 C C52 N N N 0 9.913 -10.288 17.817
27 S1 S S1 N N N 0 11.496 -11.078 17.363
28 C51 C C51 N N N 0 10.877 -12.65 16.702
29 C50 C C50 N N N 0 10.26 -12.312 15.534
30 N49 N N49 N N N 0 8.971 -12.329 15.329
31 C49 C C49 N N N 0 8.011 -12.703 16.136
32 O49 O O49 N N N 0 8.14 -13.112 17.292
33 C48 C C48 N N N 0 6.671 -12.6 15.446
34 C47 C C47 N N N 0 5.928 -13.942 15.525
35 N46 N N46 N N N 0 6.791 -15.105 15.176
36 C46 C C46 N N N 0 7.239 -15.368 13.963
37 O46 O O46 N N N 0 6.988 -14.678 12.977
38 C45 C C45 R N N 0 8.113 -16.624 13.848
39 O45 O O45 N N N 0 7.784 -17.588 14.896
40 C42 C C42 N N N 0 9.64 -16.318 13.822
41 C43 C C43 N N N 0 10.161 -15.999 15.249
42 C44 C C44 N N N 0 9.989 -15.142 12.827
43 C41 C C41 N N N 0 10.343 -17.62 13.349
44 O33 O O33 N N N 0 9.943 -17.946 11.989
45 P3 P P3 S N N 0 9.978 -19.392 11.322
46 O31 O O31 N N N 0 9.981 -19.26 9.857
47 O32 O O32 N N N 0 8.938 -20.242 11.978
48 O24 O O24 N N N 0 11.396 -20.04 11.827
49 P2 P P2 R N N 0 12.211 -21.248 11.046
50 O22 O O22 N N N 0 13.169 -20.669 10.092
51 O23 O O23 N N N 0 11.257 -22.283 10.563
52 O21 O O21 N N N 0 12.976 -21.716 12.385
53 C15 C C15 N N N 0 14.379 -21.421 12.593
54 C14 C C14 R N N 0 14.971 -22.264 13.716
55 O17 O O17 N N N 0 14.249 -21.955 14.955
56 C13 C C13 S N N 0 14.787 -23.754 13.39
57 O13 O O13 N N N 0 15.958 -24.542 13.741
58 P1 P P1 N N N 0 17.244 -24.841 12.649
59 O16 O O16 N N N 0 16.633 -25.604 11.344
60 O14 O O14 N N N 0 18.283 -25.882 13.39
61 O15 O O15 N N N 0 17.928 -23.633 12.143
62 C12 C C12 R N N 0 13.576 -24.088 14.234
63 O12 O O12 N N N 0 13.651 -25.485 14.54
64 C11 C C11 R N N 0 13.634 -23.093 15.463
65 N1 N N1 N Y N 0 12.231 -22.756 15.892
66 C1 C C1 N Y N 0 11.296 -22.168 15.134
67 N2 N N2 N Y N 0 10.154 -22.063 15.808
68 C2 C C2 N Y N 0 10.339 -22.609 17.0
69 C5 C C5 N Y N 0 11.657 -23.052 17.053
70 N5 N N5 N Y N 0 12.113 -23.656 18.171
71 C4 C C4 N Y N 0 11.317 -23.819 19.22
72 N4 N N4 N Y N 0 10.049 -23.412 19.192
73 C3 C C3 N Y N 0 9.512 -22.814 18.115
74 N3 N N3 N N N 0 8.23 -22.428 18.146
75 H56 H H56 N N N 0 9.527 -1.308 17.464
76 H66 H H66 N N N 0 11.154 0.032 16.618
77 H64 H H64 N N N 0 12.304 0.986 14.499
78 H65 H H65 N N N 0 10.211 -1.151 13.977
79 H61 H H61 N N N 0 11.252 -2.845 15.573
80 H55 H H55 N N N 0 9.398 1.07 15.345
81 H531 H 1H53 N N N 0 11.736 1.411 12.391
82 H532 H 2H53 N N N 0 12.547 0.051 11.993
83 H631 H 1H63 N N N 0 12.737 -1.845 13.42
84 H632 H 2H63 N N N 0 13.989 -0.591 13.833
85 H60 H H60 N N N 0 10.082 -2.675 18.145
86 H62 H H62 N N N 0 13.434 -0.719 16.155
87 H521 H 1H52 N N N 0 14.305 -3.013 14.753
88 H522 H 2H52 N N N 0 14.912 -2.316 16.099
89 HA H HA N N N 0 10.676 -3.868 20.183
90 H59 H H59 N N N 0 12.97 -4.779 17.102
91 H501 H 1H50 N N N 0 11.839 -2.197 21.236
92 H502 H 2H50 N N N 0 12.64 -1.725 19.894
93 HB H HB N N N 0 13.552 -3.858 19.17
94 H51 H H51 N N N 0 14.059 -4.666 21.055
95 H57 H H57 N N N 0 11.501 -6.147 19.413
96 H52 H H52 N N N 0 13.729 -6.74 18.06
97 H581 H 1H58 N N N 0 11.63 -5.987 15.462
98 H582 H 2H58 N N N 0 12.837 -6.978 16.371
99 HC H HC N N N 0 10.314 -7.147 17.694
100 HA1 H 1HA N N N 0 8.663 -8.639 17.205
101 HB2 H 2HB N N N 0 8.976 -9.903 15.923
102 HB1 H 1HB N N N 0 10.06 -9.731 18.754
103 HC2 H 2HC N N N 0 9.161 -11.084 17.922
104 H511 H 1H51 N N N 0 11.7 -13.358 16.525
105 H512 H 2H51 N N N 0 10.194 -13.155 17.402
106 H50 H H50 N N N 0 10.889 -12.005 14.712
107 H481 H 1H48 N N N 0 6.069 -11.823 15.939
108 H482 H 2H48 N N N 0 6.831 -12.34 14.389
109 H471 H 1H47 N N N 0 5.566 -14.077 16.555
110 H472 H 2H47 N N N 0 5.105 -13.909 14.796
111 H46 H H46 N N N 0 7.049 -15.73 15.913
112 H45 H H45 N N N 0 7.879 -17.072 12.871
113 HD H HD N N N 0 7.713 -18.456 14.517
114 H431 H 1H43 N N N 0 11.258 -15.924 15.231
115 H432 H 2H43 N N N 0 9.734 -15.045 15.59
116 H433 H 3H43 N N N 0 9.86 -16.803 15.937
117 H441 H 1H44 N N N 0 10.07 -14.199 13.387
118 H442 H 2H44 N N N 0 10.946 -15.356 12.328
119 H443 H 3H44 N N N 0 9.194 -15.052 12.072
120 H411 H 1H41 N N N 0 11.433 -17.474 13.38
121 H412 H 2H41 N N N 0 10.052 -18.446 14.015
122 H32 H H32 N N N 0 9.195 -20.422 12.875
123 H23 H H23 N N N 0 11.054 -22.125 9.649
124 H151 H 1H15 N N N 0 14.927 -21.635 11.664
125 H152 H 2H15 N N N 0 14.47 -20.361 12.873
126 H14 H H14 N N N 0 16.043 -22.043 13.828
127 H13 H H13 N N N 0 14.655 -23.973 12.32
128 H11 H H11 N N N 0 14.166 -23.512 16.33
129 H12 H H12 N N N 0 12.595 -23.949 13.757
130 H16 H H16 N N N 0 16.514 -24.979 10.638
131 HE H HE N N N 0 18.483 -26.602 12.803
132 HF H HF N N N 0 13.668 -25.986 13.733
133 H1 H H1 N N N 0 11.448 -21.828 14.12
134 H4 H H4 N N N 0 11.704 -24.29 20.112
135 H3N1 H 1H3N N N N 0 7.933 -22.332 19.096
136 H3N2 H 2H3N N N N 0 8.135 -21.55 17.677



BSJ : Chemical Bonds

Total Number of Bonds: 140
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O56 C66 O C sing 1.42 N N
2 C66 C65 C C sing 1.54 N N
3 C66 C61 C C sing 1.56 N N
4 C65 O55 C O sing 1.45 N N
5 C65 C64 C C sing 1.55 N N
6 C64 N53 C N sing 1.48 N N
7 C64 C63 C C sing 1.55 N N
8 C63 C62 C C sing 1.55 N N
9 C62 N52 C N sing 1.48 N N
10 C62 C61 C C sing 1.54 N N
11 C61 O54 C O sing 1.44 N N
12 O54 C60 O C sing 1.45 N N
13 C60 O53 C O sing 1.46 N N
14 C60 C55 C C sing 1.54 N N
15 O53 C59 O C sing 1.44 N N
16 C55 N50 C N sing 1.48 N N
17 C55 C56 C C sing 1.54 N N
18 C56 O51 C O sing 1.43 N N
19 C56 C57 C C sing 1.54 N N
20 C57 O52 C O sing 1.42 N N
21 C57 C59 C C sing 1.55 N N
22 C59 C58 C C sing 1.54 N N
23 C58 N51 C N sing 1.47 N N
24 N51 C54 N C sing 1.34 N N
25 C54 O57 C O doub 1.24 N N
26 C54 C53 C C sing 1.55 N N
27 C53 C52 C C sing 1.54 N N
28 C52 S1 C S sing 1.83 N N
29 S1 C51 S C sing 1.81 N N
30 C51 C50 C C sing 1.36 N N
31 C50 N49 C N doub 1.31 N N
32 N49 C49 N C sing 1.31 N N
33 C49 O49 C O doub 1.23 N N
34 C49 C48 C C sing 1.51 N N
35 C48 C47 C C sing 1.54 N N
36 C47 N46 C N sing 1.49 N N
37 N46 C46 N C sing 1.32 N N
38 C46 O46 C O doub 1.23 N N
39 C46 C45 C C sing 1.53 N N
40 C45 O45 C O sing 1.46 N N
41 C45 C42 C C sing 1.56 N N
42 C42 C43 C C sing 1.55 N N
43 C42 C44 C C sing 1.58 N N
44 C42 C41 C C sing 1.55 N N
45 C41 O33 C O sing 1.45 N N
46 O33 P3 O P sing 1.59 N N
47 P3 O31 P O doub 1.47 N N
48 P3 O32 P O sing 1.49 N N
49 P3 O24 P O sing 1.64 N N
50 O24 P2 O P sing 1.65 N N
51 P2 O22 P O doub 1.47 N N
52 P2 O23 P O sing 1.49 N N
53 P2 O21 P O sing 1.61 N N
54 O21 C15 O C sing 1.45 N N
55 C15 C14 C C sing 1.52 N N
56 C14 O17 C O sing 1.47 N N
57 C14 C13 C C sing 1.54 N N
58 O17 C11 O C sing 1.39 N N
59 C13 O13 C O sing 1.45 N N
60 C13 C12 C C sing 1.51 N N
61 O13 P1 O P sing 1.71 N N
62 P1 O16 P O sing 1.63 N N
63 P1 O14 P O sing 1.65 N N
64 P1 O15 P O doub 1.48 N N
65 C12 O12 C O sing 1.43 N N
66 C12 C11 C C sing 1.58 N N
67 C11 N1 C N sing 1.51 N N
68 N1 C1 N C sing 1.34 N Y
69 N1 C5 N C sing 1.33 N Y
70 C1 N2 C N doub 1.33 N Y
71 N2 C2 N C sing 1.32 N Y
72 C2 C5 C C sing 1.39 N Y
73 C2 C3 C C doub 1.4 N Y
74 C5 N5 C N doub 1.35 N Y
75 N5 C4 N C sing 1.33 N Y
76 C4 N4 C N doub 1.33 N Y
77 N4 C3 N C sing 1.34 N Y
78 C3 N3 C N sing 1.34 N N
79 O56 H56 O H sing 0.95 N N
80 C66 H66 C H sing 1.1 N N
81 C65 H65 C H sing 1.1 N N
82 C61 H61 C H sing 1.1 N N
83 O55 H55 O H sing 0.95 N N
84 C64 H64 C H sing 1.1 N N
85 N53 H531 N H sing 1.0 N N
86 N53 H532 N H sing 1.0 N N
87 C63 H631 C H sing 1.1 N N
88 C63 H632 C H sing 1.1 N N
89 C62 H62 C H sing 1.1 N N
90 N52 H521 N H sing 1.0 N N
91 N52 H522 N H sing 1.0 N N
92 C60 H60 C H sing 1.1 N N
93 C55 HA C H sing 1.1 N N
94 C59 H59 C H sing 1.1 N N
95 N50 H501 N H sing 1.0 N N
96 N50 H502 N H sing 1.0 N N
97 C56 HB C H sing 1.1 N N
98 O51 H51 O H sing 0.95 N N
99 C57 H57 C H sing 1.1 N N
100 O52 H52 O H sing 0.95 N N
101 C58 H581 C H sing 1.1 N N
102 C58 H582 C H sing 1.1 N N
103 N51 HC N H sing 1.0 N N
104 C53 HA1 C H sing 1.1 N N
105 C53 HB2 C H sing 1.1 N N
106 C52 HB1 C H sing 1.1 N N
107 C52 HC2 C H sing 1.1 N N
108 C51 H511 C H sing 1.1 N N
109 C51 H512 C H sing 1.1 N N
110 C50 H50 C H sing 1.08 N N
111 C48 H481 C H sing 1.1 N N
112 C48 H482 C H sing 1.1 N N
113 C47 H471 C H sing 1.1 N N
114 C47 H472 C H sing 1.1 N N
115 N46 H46 N H sing 1.0 N N
116 C45 H45 C H sing 1.1 N N
117 O45 HD O H sing 0.95 N N
118 C43 H431 C H sing 1.1 N N
119 C43 H432 C H sing 1.1 N N
120 C43 H433 C H sing 1.1 N N
121 C44 H441 C H sing 1.1 N N
122 C44 H442 C H sing 1.1 N N
123 C44 H443 C H sing 1.1 N N
124 C41 H411 C H sing 1.1 N N
125 C41 H412 C H sing 1.1 N N
126 O32 H32 O H sing 0.95 N N
127 O23 H23 O H sing 0.95 N N
128 C15 H151 C H sing 1.1 N N
129 C15 H152 C H sing 1.1 N N
130 C14 H14 C H sing 1.1 N N
131 C13 H13 C H sing 1.1 N N
132 C11 H11 C H sing 1.1 N N
133 C12 H12 C H sing 1.1 N N
134 O16 H16 O H sing 0.95 N N
135 O14 HE O H sing 0.95 N N
136 O12 HF O H sing 0.95 N N
137 C1 H1 C H sing 1.08 N N
138 C4 H4 C H sing 1.08 N N
139 N3 H3N1 N H sing 1.0 N N
140 N3 H3N2 N H sing 1.0 N N



BSJ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
BSJ 2vbq Open in New Window Bound ligand 2 1