Chemical Components in the PDB

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1CV : Summary

Code

1CV

One-letter code

X

Molecule name

(3R,5R,9R,19R,21S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,21-tetrahydroxy-8,8,21-trimethyl-10,14-dioxo-19-sulfanyl-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphatricosan-23-oic acid 3,5-dioxide

Systematic names

ProgramVersionName
ACDLabs 12.01 (3R,5R,9R,19R,21S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,21-tetrahydroxy-8,8,21-trimethyl-10,14-dioxo-19-sulfanyl-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphatricosan-23-oic acid 3,5-dioxide
OpenEye OEToolkits 1.7.6 (3S,5R)-5-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-3-methyl-3-oxidanyl-5-sulfanyl-pentanoic acid

Formula

C27 H46 N7 O19 P3 S2

Formal charge

0

Molecular weight

929.741 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)CC(O)(C)CC(S)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
SMILES CACTVS 3.370 C[C](O)(C[CH](S)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)CC(O)=O
SMILES OpenEye OEToolkits 1.7.6 CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(CC(C)(CC(=O)O)O)S)O
Canonical SMILES CACTVS 3.370 C[C@@](O)(C[C@H](S)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(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)CC(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@@](C[C@H](S)SCCNC(=O)CCNC(=O)[C@@H](C(C)(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)O)(CC(=O)O)O

IUPAC InChI

InChI=1S/C27H46N7O19P3S2/c1-26(2,21(39)24(40)30-5-4-15(35)29-6-7-58-17(57)9-27(3,41)8-16(36)37)11-50-56(47,48)53-55(45,46)49-10-14-20(52-54(42,43)44)19(38)25(51-14)34-13-33-18-22(28)31-12-32-23(18)34/h12-14,17,19-21,25,38-39,41,57H,4-11H2,1-3H3,(H,29,35)(H,30,40)(H,36,37)(H,45,46)(H,47,48)(H2,28,31,32)(H2,42,43,44)/t14-,17-,19-,20-,21+,25-,27+/m1/s1

IUPAC InChI key

YDFKRXILVYQATJ-NLYQEGKRSA-N
1CV

wwPDB Information

Atom count

104 (58 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-12-07

Last modified at

2013-07-12

Status

Released

Obsoleted

Not Assigned



1CV : Atoms of Molecule

Total Number of Atoms: 104
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 R N N 0 10.764 -1.52 0.448
2 C1' C C1* R N N 0 -7.168 -2.502 -0.657
3 C10 C C10 R N N 0 1.222 6.198 -2.573
4 C11 C C11 N N N 0 0.116 5.157 -2.385
5 C12 C C12 N N N 0 -0.391 5.205 -0.942
6 C13 C C13 N N N 0 -1.039 5.462 -3.342
7 C14 C C14 N N N 0 0.671 3.763 -2.685
8 C2 C C2 N N N 0 11.804 -2.076 1.423
9 C2' C C2* R N N 0 -7.938 -2.724 0.67
10 C2A C C2A N Y N 0 -8.247 -6.256 -2.87
11 C2P C C2P N N N 0 8.679 0.345 -0.033
12 C3 C C3 S N N 0 12.393 -3.37 0.858
13 C3' C C3* S N N 0 -8.102 -1.276 1.195
14 C3P C C3P N N N 0 7.897 1.57 0.449
15 C4 C C4 N N N 0 13.34 -3.991 1.887
16 C4' C C4* R N N 0 -7.003 -0.482 0.463
17 C4A C C4A N Y N 0 -6.907 -4.786 -1.717
18 C5 C C5 N N N 0 13.92 -5.266 1.331
19 C5' C C5* N N N 0 -6.066 0.17 1.482
20 C5A C C5A N Y N 0 -5.835 -5.687 -1.835
21 C5P C C5P N N N 0 6.046 2.956 -0.319
22 C6 C C6 N N N 0 11.262 -4.352 0.547
23 C6A C C6A N Y N 0 -6.059 -6.898 -2.511
24 C6P C C6P N N N 0 4.981 3.301 -1.328
25 C7P C C7P N N N 0 4.2 4.525 -0.847
26 C8A C C8A N Y N 0 -5.109 -3.958 -0.745
27 C9P C C9P N N N 0 2.349 5.911 -1.614
28 H1 H H1 N N N 0 10.015 -2.285 0.241
29 H1' H H1* N N N 0 -7.854 -2.219 -1.455
30 H10 H H10 N N N 0 1.595 6.151 -3.596
31 H12 H H12 N N N 0 0.432 4.988 -0.261
32 H12A H H12A N N N 0 -0.786 6.198 -0.729
33 H13 H H13 N N N 0 -0.691 5.374 -4.371
34 H13A H H13A N N N 0 -1.849 4.754 -3.17
35 H13B H H13B N N N 0 -1.398 6.476 -3.165
36 H14 H H14 N N N 0 1.403 3.492 -1.923
37 H14A H H14A N N N 0 -0.143 3.039 -2.68
38 H14B H H14B N N N 0 1.15 3.765 -3.664
39 H2 H H2 N N N 0 12.599 -1.344 1.562
40 H2' H H2* N N N 0 -7.351 -3.325 1.365
41 H2A H H2A N N N 0 11.328 -2.282 2.382
42 H2AA H H2AA N N N 0 -9.215 -6.487 -3.287
43 H2P H H2P N N N 0 9.146 0.567 -0.992
44 H2PA H H2PA N N N 0 7.998 -0.498 -0.146
45 H3' H H3* N N N 0 -7.947 -1.242 2.273
46 H3P H H3P N N N 0 7.43 1.349 1.408
47 H3PA H H3PA N N N 0 8.578 2.414 0.562
48 H4 H H4 N N N 0 14.145 -3.291 2.109
49 H4' H H4* N N N 0 -7.456 0.282 -0.169
50 H4A H H4A N N N 0 12.788 -4.212 2.801
51 H5' H H5* N N N 0 -6.649 0.778 2.174
52 H5'A H H5*A N N N 0 -5.536 -0.605 2.036
53 H6 H H6 N N N 0 10.588 -3.91 -0.186
54 H6A H H6A N N N 0 11.682 -5.274 0.145
55 H6B H H6B N N N 0 10.711 -4.573 1.461
56 H6P H H6P N N N 0 5.449 3.522 -2.288
57 H6PA H H6PA N N N 0 4.301 2.457 -1.441
58 H7P H H7P N N N 0 3.733 4.304 0.113
59 H7PA H H7PA N N N 0 4.881 5.369 -0.734
60 H8A H H8A N N N 0 -4.451 -3.292 -0.207
61 HN4P H HN4P N N N 0 6.765 1.371 -1.337
62 HN6A H HN6A N N N 0 -4.161 -7.641 -2.294
63 HN6B H HN6B N N N 0 -5.208 -8.657 -3.128
64 HN8P H HN8P N N N 0 3.068 4.327 -2.632
65 HO10 H HO10 N N N 0 0.347 7.615 -1.421
66 HO2' H HO2* N N N 0 -9.16 -4.199 0.014
67 HO2A H HO2A N N N 0 -2.503 0.227 1.66
68 HO4 H HO4 N N N 0 15.129 -6.796 1.664
69 HO4A H HO4A N N N 0 -3.697 5.566 0.35
70 HO7 H HO7 N N N 0 13.849 -2.463 -0.218
71 HO8A H HO8A N N N 0 -9.676 1.791 2.114
72 HO9A H HO9A N N N 0 -12.52 0.444 1.852
73 HS2 H HS2 N N N 0 12.464 -0.108 -0.697
74 N1A N N1A N Y N 0 -7.269 -7.134 -3.006
75 N3A N N3A N Y N 0 -8.083 -5.109 -2.245
76 N4P N N4P N N N 0 6.862 1.905 -0.533
77 N6A N N6A N N N 0 -5.041 -7.825 -2.659
78 N7A N N7A N Y N 0 -4.769 -5.121 -1.221
79 N8P N N8P N N N 0 3.165 4.861 -1.828
80 N9A N N9A N Y N 0 -6.419 -3.706 -1.026
81 O10 O O10 N N N 0 0.697 7.502 -2.316
82 O1A O O1A N N N 0 -4.608 2.704 2.587
83 O2' O O2* N N N 0 -9.21 -3.326 0.428
84 O2A O O2A N N N 0 -2.951 0.826 2.273
85 O3 O O3 N N N 0 13.609 -5.639 0.224
86 O3' O O3* N N N 0 -9.394 -0.767 0.86
87 O3A O O3A N N N 0 -3.188 2.753 0.501
88 O4 O O4 N N N 0 14.783 -5.986 2.064
89 O4' O O4* N N N 0 -6.27 -1.415 -0.348
90 O4A O O4A N N N 0 -3.027 5.328 1.005
91 O5' O O5* N N N 0 -5.122 0.998 0.8
92 O5A O O5A N N N 0 -1.194 3.736 1.696
93 O5P O O5P N N N 0 6.167 3.623 0.687
94 O6A O O6A N N N 0 -1.423 4.233 -0.767
95 O7 O O7 N N N 0 13.116 -3.081 -0.34
96 O7A O O7A N N N 0 -10.682 -1.324 2.959
97 O8A O O8A N N N 0 -9.855 1.048 2.706
98 O9A O O9A N N N 0 -11.837 0.126 1.246
99 O9P O O9P N N N 0 2.52 6.626 -0.65
100 P1A P P1A N N N 0 -3.981 1.839 1.562
101 P2A P P2A N N N 0 -2.186 4.007 0.632
102 P3' P P3* N N N 0 -10.447 -0.253 1.965
103 S1P S S1P N N N 0 9.96 -0.07 1.183
104 S2 S S2 N N N 0 11.582 -1.04 -1.099



1CV : Chemical Bonds

Total Number of Bonds: 106
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 S1P C1 S C sing 1.81 N N
2 C1 C2 C C sing 1.53 N N
3 C1 S2 C S sing 1.81 N N
4 C1 H1 C H sing 1.09 N N
5 C3 C2 C C sing 1.53 N N
6 C2 H2 C H sing 1.09 N N
7 C2 H2A C H sing 1.09 N N
8 S2 HS2 S H sing 1.34 N N
9 C6 C3 C C sing 1.53 N N
10 O7 C3 O C sing 1.43 N N
11 C3 C4 C C sing 1.53 N N
12 O3 C5 O C doub 1.21 N N
13 C5 C4 C C sing 1.51 N N
14 C4 H4 C H sing 1.09 N N
15 C4 H4A C H sing 1.09 N N
16 C5 O4 C O sing 1.34 N N
17 O4 HO4 O H sing 0.97 N N
18 C6 H6 C H sing 1.09 N N
19 C6 H6A C H sing 1.09 N N
20 C6 H6B C H sing 1.09 N N
21 O7 HO7 O H sing 0.97 N N
22 O4' C1' O C sing 1.44 N N
23 N9A C1' N C sing 1.47 N N
24 C1' C2' C C sing 1.55 N N
25 C1' H1' C H sing 1.09 N N
26 O10 C10 O C sing 1.43 N N
27 C10 C11 C C sing 1.53 N N
28 C10 C9P C C sing 1.51 N N
29 C10 H10 C H sing 1.09 N N
30 O10 HO10 O H sing 0.97 N N
31 C12 C11 C C sing 1.53 N N
32 C11 C13 C C sing 1.53 N N
33 C11 C14 C C sing 1.53 N N
34 O6A C12 O C sing 1.43 N N
35 C12 H12 C H sing 1.09 N N
36 C12 H12A C H sing 1.09 N N
37 C13 H13 C H sing 1.09 N N
38 C13 H13A C H sing 1.09 N N
39 C13 H13B C H sing 1.09 N N
40 C14 H14 C H sing 1.09 N N
41 C14 H14A C H sing 1.09 N N
42 C14 H14B C H sing 1.09 N N
43 C6A N1A C N doub 1.33 N Y
44 N1A C2A N C sing 1.32 N Y
45 O1A P1A O P doub 1.48 N N
46 O3A P1A O P sing 1.61 N N
47 O2A P1A O P sing 1.61 N N
48 P1A O5' P O sing 1.61 N N
49 S1P C2P S C sing 1.81 N N
50 C3' C2' C C sing 1.55 N N
51 C2' O2' C O sing 1.43 N N
52 C2' H2' C H sing 1.09 N N
53 O2' HO2' O H sing 0.97 N N
54 N3A C2A N C doub 1.32 N Y
55 C2A H2AA C H sing 1.08 N N
56 O2A HO2A O H sing 0.97 N N
57 O5A P2A O P doub 1.48 N N
58 O4A P2A O P sing 1.61 N N
59 P2A O3A P O sing 1.61 N N
60 P2A O6A P O sing 1.61 N N
61 C2P C3P C C sing 1.53 N N
62 C2P H2P C H sing 1.09 N N
63 C2P H2PA C H sing 1.09 N N
64 C4' C3' C C sing 1.54 N N
65 C3' O3' C O sing 1.43 N N
66 C3' H3' C H sing 1.09 N N
67 P3' O3' P O sing 1.61 N N
68 O7A P3' O P doub 1.48 N N
69 O9A P3' O P sing 1.61 N N
70 P3' O8A P O sing 1.61 N N
71 C4A N3A C N sing 1.33 N Y
72 N4P C3P N C sing 1.47 N N
73 C3P H3P C H sing 1.09 N N
74 C3P H3PA C H sing 1.09 N N
75 C5' C4' C C sing 1.53 N N
76 C4' O4' C O sing 1.44 N N
77 C4' H4' C H sing 1.09 N N
78 C5A C4A C C doub 1.41 N Y
79 N9A C4A N C sing 1.37 N Y
80 O4A HO4A O H sing 0.97 N N
81 C5P N4P C N sing 1.35 N N
82 N4P HN4P N H sing 0.97 N N
83 O5' C5' O C sing 1.43 N N
84 C5' H5' C H sing 1.09 N N
85 C5' H5'A C H sing 1.09 N N
86 N7A C5A N C sing 1.35 N Y
87 C5A C6A C C sing 1.4 N Y
88 C6P C5P C C sing 1.51 N N
89 C5P O5P C O doub 1.21 N N
90 N6A C6A N C sing 1.38 N N
91 N6A HN6A N H sing 0.97 N N
92 N6A HN6B N H sing 0.97 N N
93 C7P C6P C C sing 1.53 N N
94 C6P H6P C H sing 1.09 N N
95 C6P H6PA C H sing 1.09 N N
96 N7A C8A N C doub 1.3 N Y
97 N8P C7P N C sing 1.47 N N
98 C7P H7P C H sing 1.09 N N
99 C7P H7PA C H sing 1.09 N N
100 C8A N9A C N sing 1.36 N Y
101 C8A H8A C H sing 1.08 N N
102 O8A HO8A O H sing 0.97 N N
103 N8P C9P N C sing 1.35 N N
104 N8P HN8P N H sing 0.97 N N
105 O9A HO9A O H sing 0.97 N N
106 C9P O9P C O doub 1.21 N N



1CV : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
1CV 4i4b Open in New Window Bound ligand 1 1