Chemical Components in the PDB

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25L : Summary

Code

25L

One-letter code

X

Molecule name

[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate

Synonyms

2'-5'-oligoadenylate trimer

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.6.1 [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate

Formula

C30 H40 N15 O25 P5

Formal charge

0

Molecular weight

1165.593 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.352 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[CH]4[CH](O)[CH](CO[P](O)(=O)O[CH]5[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O[CH]5n6cnc7c(N)ncnc67)O[CH]4n8cnc9c(N)ncnc89)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 1.7.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC4C(C(OC4n5cnc6c5ncnc6N)COP(=O)(O)OC7C(C(OC7n8cnc9c8ncnc9N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)O)O)N
Canonical SMILES CACTVS 3.352 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[C@@H]4[C@H](O)[C@@H](CO[P](O)(=O)O[C@@H]5[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O[C@H]5n6cnc7c(N)ncnc67)O[C@H]4n8cnc9c(N)ncnc89)[C@@H](O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 1.7.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[C@@H]4[C@@H]([C@H](O[C@H]4n5cnc6c5ncnc6N)CO[P@](=O)(O)O[C@@H]7[C@@H]([C@H](O[C@H]7n8cnc9c8ncnc9N)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)O)O)O)N

IUPAC InChI

InChI=1S/C30H40N15O25P5/c31-22-13-25(37-4-34-22)43(7-40-13)28-19(49)16(46)10(64-28)1-61-72(53,54)67-20-17(47)11(65-29(20)44-8-41-14-23(32)35-5-38-26(14)44)2-62-73(55,56)68-21-18(48)12(3-63-74(57,58)70-75(59,60)69-71(50,51)52)66-30(21)45-9-42-15-24(33)36-6-39-27(15)45/h4-12,16-21,28-30,46-49H,1-3H2,(H,53,54)(H,55,56)(H,57,58)(H,59,60)(H2,31,34,37)(H2,32,35,38)(H2,33,36,39)(H2,50,51,52)/t10-,11-,12-,16-,17-,18-,19-,20-,21-,28-,29-,30-/m1/s1

IUPAC InChI key

RTAGLZBJCCVJET-UQTMIEBXSA-N
25L

wwPDB Information

Atom count

115 (75 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-09-15

Last modified at

2014-01-31

Status

Released

Obsoleted

Not Assigned



25L : Atoms of Molecule

Total Number of Atoms: 115
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 -12.788 -6.465 0.191
2 C2 C C2 N Y N 0 -13.078 -5.768 -0.893
3 N3 N N3 N Y N 0 -12.517 -4.608 -1.159
4 C4 C C4 N Y N 0 -11.619 -4.084 -0.33
5 C5 C C5 N Y N 0 -11.276 -4.786 0.838
6 C6 C C6 N Y N 0 -11.903 -6.021 1.077
7 N6 N N6 N N N 0 -11.606 -6.758 2.211
8 N7 N N7 N Y N 0 -10.354 -4.043 1.495
9 C8 C C8 N Y N 0 -10.116 -2.955 0.822
10 N9 N N9 N Y N 0 -10.872 -2.934 -0.312
11 C1' C C1* R N N 0 -10.884 -1.877 -1.327
12 C2' C C2* R N N 0 -12.031 -0.871 -1.054
13 O2' O O2* N N N 0 -13.252 -1.318 -1.647
14 C3' C C3* S N N 0 -11.513 0.409 -1.753
15 O3' O O3* N N N 0 -12.091 0.538 -3.054
16 C4' C C4* R N N 0 -9.991 0.193 -1.858
17 O4' O O4* N N N 0 -9.694 -1.065 -1.229
18 C5' C C5* N N N 0 -9.254 1.323 -1.136
19 O5' O O5* N N N 0 -7.847 1.179 -1.337
20 NAB N NAB N N N 0 4.759 6.535 3.224
21 NAC N NAC N N N 0 -5.098 1.109 6.044
22 OAD O OAD N N N 0 14.229 -5.024 0.397
23 OAE O OAE N N N 0 10.637 -0.35 -2.289
24 OAF O OAF N N N 0 -6.954 2.287 0.747
25 OAG O OAG N N N 0 2.206 3.826 -1.139
26 OAH O OAH N N N 0 12.848 -2.951 -1.4
27 OAK O OAK N N N 0 4.28 -0.171 -3.024
28 OAL O OAL N N N 0 -3.763 2.384 -2.946
29 OAM O OAM N N N 0 9.733 -2.598 -3.0
30 OAN O OAN N N N 0 12.745 -5.82 2.276
31 OAO O OAO N N N 0 14.294 -3.714 2.553
32 OAP O OAP N N N 0 -6.957 3.652 -1.376
33 OAQ O OAQ N N N 0 2.156 2.918 -3.494
34 OAR O OAR N N N 0 12.833 -1.13 0.348
35 CAT C CAT N Y N 0 2.474 3.859 2.587
36 CAU C CAU N Y N 0 -6.234 -0.539 3.083
37 CAW C CAW N Y N 0 6.409 3.558 0.573
38 CAX C CAX N Y N 0 -2.788 2.198 2.567
39 CAY C CAY N N N 0 7.512 -0.305 -2.247
40 CBA C CBA N N N 0 -0.659 2.778 -1.817
41 NBC N NBC N Y N 0 2.994 4.979 3.057
42 NBD N NBD N Y N 0 -6.131 -0.155 4.342
43 NBF N NBF N Y N 0 3.135 3.06 1.776
44 NBG N NBG N Y N 0 -5.429 -0.096 2.14
45 NBI N NBI N Y N 0 6.21 4.6 1.326
46 NBJ N NBJ N Y N 0 -3.274 2.081 3.769
47 OBK O OBK N N N 0 8.383 -1.03 -1.378
48 OBM O OBM N N N 0 0.53 2.006 -1.64
49 OBO O OBO N N N 0 6.429 0.91 -0.426
50 OBP O OBP N N N 0 -1.878 1.615 -0.049
51 OBQ O OBQ N N N 0 3.105 1.495 -1.498
52 OBR O OBR N N N 0 -5.28 1.657 -1.033
53 OBS O OBS N N N 0 12.212 -3.613 0.951
54 OBT O OBT N N N 0 10.598 -2.182 -0.552
55 CBV C CBV N Y N 0 4.224 5.359 2.727
56 CBW C CBW N Y N 0 -5.197 0.711 4.723
57 CBY C CBY N Y N 0 4.968 4.539 1.863
58 CBZ C CBZ N Y N 0 -4.314 1.213 3.752
59 CCB C CCB N Y N 0 4.371 3.357 1.391
60 CCC C CCC N Y N 0 -4.465 0.772 2.427
61 CCF C CCF R N N 0 5.223 0.74 -2.458
62 CCG C CCG R N N 0 -3.18 2.725 -1.687
63 CCI C CCI R N N 0 6.2 -0.0040 -1.52
64 CCJ C CCJ R N N 0 -1.878 1.925 -1.459
65 CCK C CCK R N N 0 4.511 1.751 -1.532
66 CCL C CCL R N N 0 -4.1 2.284 -0.527
67 CCN C CCN R N N 0 5.141 1.497 -0.144
68 CCO C CCO R N N 0 -3.245 1.27 0.265
69 NCQ N NCQ N Y N 0 5.304 2.76 0.58
70 NCR N NCR N Y N 0 -3.489 1.41 1.703
71 PCS P PCS N N N 0 13.388 -4.553 1.52
72 PCT P PCT N N N 0 9.855 -1.515 -1.815
73 PCU P PCU N N N 0 -6.764 2.196 -0.718
74 PCV P PCV N N N 0 2.004 2.588 -1.926
75 PCW P PCW N N N 0 12.138 -2.479 -0.19
76 H2 H H2 N N N 0 -13.803 -6.166 -1.588
77 HN6 H HN6 N N N 0 -12.045 -7.609 2.365
78 HN6A H HN6A N N N 0 -10.958 -6.424 2.85
79 H8 H H8 N N N 0 -9.421 -2.183 1.118
80 H1' H H1* N N N 0 -10.977 -2.305 -2.325
81 H2' H H2* N N N 0 -12.158 -0.707 0.016
82 HO2' H HO2* N N N 0 -14.0 -0.722 -1.504
83 H3' H H3* N N N 0 -11.735 1.29 -1.149
84 HO3' H HO3* N N N 0 -13.055 0.618 -3.05
85 H4' H H4* N N N 0 -9.692 0.163 -2.906
86 H5' H H5* N N N 0 -9.581 2.283 -1.535
87 H5'A H H5*A N N N 0 -9.475 1.278 -0.07
88 HNAB H HNAB N N N 0 4.235 7.092 3.82
89 HNAA H HNAA N N N 0 5.658 6.801 2.976
90 HNAC H HNAC N N N 0 -5.714 0.755 6.705
91 HNAD H HNAD N N N 0 -4.412 1.742 6.31
92 HOAK H HOAK N N N 0 4.68 -0.865 -3.567
93 HOAL H HOAL N N N 0 -3.201 2.584 -3.707
94 HOAM H HOAM N N N 0 9.232 -3.389 -2.76
95 HOAN H HOAN N N N 0 13.397 -6.431 2.645
96 HOAO H HOAO N N N 0 13.807 -3.374 3.316
97 HOAP H HOAP N N N 0 -6.847 3.668 -2.336
98 HOAQ H HOAQ N N N 0 2.036 2.151 -4.071
99 HOAR H HOAR N N N 0 12.418 -0.764 1.141
100 HAT H HAT N N N 0 1.473 3.586 2.885
101 HAU H HAU N N N 0 -7.004 -1.249 2.817
102 HAW H HAW N N N 0 7.317 3.354 0.024
103 HAX H HAX N N N 0 -1.953 2.826 2.295
104 HAY H HAY N N N 0 7.988 0.631 -2.54
105 HAYA H HAYA N N N 0 7.306 -0.902 -3.136
106 HBA H HBA N N N 0 -0.625 3.652 -1.168
107 HBAA H HBAA N N N 0 -0.733 3.099 -2.856
108 HCF H HCF N N N 0 5.771 1.26 -3.244
109 HCG H HCG N N N 0 -2.984 3.796 -1.636
110 HCI H HCI N N N 0 5.749 -0.927 -1.156
111 HCJ H HCJ N N N 0 -1.886 1.009 -2.049
112 HCK H HCK N N N 0 4.704 2.772 -1.86
113 HCL H HCL N N N 0 -4.361 3.138 0.099
114 HCN H HCN N N N 0 4.525 0.806 0.431
115 HCO H HCO N N N 0 -3.464 0.253 -0.061



25L : Chemical Bonds

Total Number of Bonds: 123
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C doub 1.3209713 N Y
2 N1 C6 N C sing 1.3286674 N Y
3 C2 N3 C N sing 1.315704 N Y
4 N3 C4 N C doub 1.3297447 N Y
5 C4 C5 C C sing 1.405232 N Y
6 C4 N9 C N sing 1.3714347 N Y
7 C5 C6 C C doub 1.4055159 N Y
8 C5 N7 C N sing 1.3541721 N Y
9 C6 N6 C N sing 1.3846782 N N
10 N7 C8 N C doub 1.3012751 N Y
11 C8 N9 C N sing 1.3630601 N Y
12 N9 C1' N C sing 1.4654753 N N
13 C1' C2' C C sing 1.5498948 N N
14 C1' O4' C O sing 1.4439695 N N
15 C2' O2' C O sing 1.4290903 N N
16 C2' C3' C C sing 1.5476837 N N
17 C3' O3' C O sing 1.4294496 N N
18 C3' C4' C C sing 1.5408325 N N
19 C4' O4' C O sing 1.4375027 N N
20 C4' C5' C C sing 1.530148 N N
21 C5' O5' C O sing 1.4285609 N N
22 O5' PCU O P sing 1.609453 N N
23 NAB CBV N C sing 1.3842723 N N
24 NAC CBW N C sing 1.3832014 N N
25 OAD PCS O P doub 1.4799497 N N
26 OAE PCT O P doub 1.4810216 N N
27 OAF PCU O P doub 1.4800696 N N
28 OAG PCV O P doub 1.4808164 N N
29 OAH PCW O P doub 1.4801973 N N
30 OAK CCF O C sing 1.4281198 N N
31 OAL CCG O C sing 1.4287236 N N
32 OAM PCT O P sing 1.6099683 N N
33 OAN PCS O P sing 1.6094328 N N
34 OAO PCS O P sing 1.6099211 N N
35 OAP PCU O P sing 1.609394 N N
36 OAQ PCV O P sing 1.6095428 N N
37 OAR PCW O P sing 1.6100528 N N
38 CAT NBC C N doub 1.3212494 N Y
39 CAT NBF C N sing 1.316451 N Y
40 CAU NBD C N doub 1.3202826 N Y
41 CAU NBG C N sing 1.3166332 N Y
42 CAW NBI C N doub 1.3009127 N Y
43 CAW NCQ C N sing 1.36304 N Y
44 CAX NBJ C N doub 1.3018022 N Y
45 CAX NCR C N sing 1.3633932 N Y
46 CAY OBK C O sing 1.4280851 N N
47 CAY CCI C C sing 1.5298607 N N
48 CBA OBM C O sing 1.4286476 N N
49 CBA CCJ C C sing 1.5302725 N N
50 NBC CBV N C sing 1.3289846 N Y
51 NBD CBW N C sing 1.3294635 N Y
52 NBF CCB N C doub 1.3282056 N Y
53 NBG CCC N C doub 1.3285666 N Y
54 NBI CBY N C sing 1.354494 N Y
55 NBJ CBZ N C sing 1.3547373 N Y
56 OBK PCT O P sing 1.6102726 N N
57 OBM PCV O P sing 1.6103404 N N
58 OBO CCI O C sing 1.4438397 N N
59 OBO CCN O C sing 1.4432731 N N
60 OBP CCJ O C sing 1.4436759 N N
61 OBP CCO O C sing 1.4444065 N N
62 OBQ CCK O C sing 1.4295202 N N
63 OBQ PCV O P sing 1.6093583 N N
64 OBR CCL O C sing 1.4288335 N N
65 OBR PCU O P sing 1.6099696 N N
66 OBS PCS O P sing 1.6094524 N N
67 OBS PCW O P sing 1.6103767 N N
68 OBT PCT O P sing 1.6100022 N N
69 OBT PCW O P sing 1.6096127 N N
70 CBV CBY C C doub 1.404433 N Y
71 CBW CBZ C C doub 1.4051812 N Y
72 CBY CCB C C sing 1.4058154 N Y
73 CBZ CCC C C sing 1.404602 N Y
74 CCB NCQ C N sing 1.3728143 N Y
75 CCC NCR C N sing 1.3725145 N Y
76 CCF CCI C C sing 1.545286 N N
77 CCF CCK C C sing 1.5448433 N N
78 CCG CCJ C C sing 1.5450528 N N
79 CCG CCL C C sing 1.5448239 N N
80 CCK CCN C C sing 1.5453025 N N
81 CCL CCO C C sing 1.5448252 N N
82 CCN NCQ C N sing 1.4648938 N N
83 CCO NCR C N sing 1.4652576 N N
84 C2 H2 C H sing 1.0803027 N N
85 N6 HN6 N H sing 0.96986496 N N
86 N6 HN6A N H sing 0.969423 N N
87 C8 H8 C H sing 1.0801041 N N
88 C1' H1' C H sing 1.0898794 N N
89 C2' H2' C H sing 1.0899197 N N
90 O2' HO2' O H sing 0.9670414 N N
91 C3' H3' C H sing 1.0909908 N N
92 O3' HO3' O H sing 0.96732205 N N
93 C4' H4' C H sing 1.0902317 N N
94 C5' H5' C H sing 1.0898303 N N
95 C5' H5'A C H sing 1.0895972 N N
96 NAB HNAB N H sing 0.9695571 N N
97 NAB HNAA N H sing 0.9697737 N N
98 NAC HNAC N H sing 0.9704087 N N
99 NAC HNAD N H sing 0.97058797 N N
100 OAK HOAK O H sing 0.9677215 N N
101 OAL HOAL O H sing 0.9669359 N N
102 OAM HOAM O H sing 0.96658266 N N
103 OAN HOAN O H sing 0.9667399 N N
104 OAO HOAO O H sing 0.9669219 N N
105 OAP HOAP O H sing 0.966414 N N
106 OAQ HOAQ O H sing 0.9672735 N N
107 OAR HOAR O H sing 0.9669695 N N
108 CAT HAT C H sing 1.0795064 N N
109 CAU HAU C H sing 1.0806276 N N
110 CAW HAW C H sing 1.0805004 N N
111 CAX HAX C H sing 1.0796263 N N
112 CAY HAY C H sing 1.0901932 N N
113 CAY HAYA C H sing 1.0904889 N N
114 CBA HBA C H sing 1.0891433 N N
115 CBA HBAA C H sing 1.0899715 N N
116 CCF HCF C H sing 1.0901835 N N
117 CCG HCG C H sing 1.0899807 N N
118 CCI HCI C H sing 1.0898743 N N
119 CCJ HCJ C H sing 1.0895963 N N
120 CCK HCK C H sing 1.0896211 N N
121 CCL HCL C H sing 1.0905563 N N
122 CCN HCN C H sing 1.0897532 N N
123 CCO HCO C H sing 1.0901954 N N



25L : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
25L 4o1o Open in New Window Bound ligand 4 1
25L 4o1p Open in New Window Bound ligand 4 1