Chemical Components in the PDB

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2NE : Summary

Code

2NE

One-letter code

X

Molecule name

Salicylyl CoA

Systematic names

ProgramVersionName
ACDLabs 12.01 S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} 2-hydroxybenzenecarbothioate (non-preferred name)
OpenEye OEToolkits 1.7.6 S-[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]ethyl] 2-oxidanylbenzenecarbothioate

Formula

C28 H40 N7 O18 P3 S

Formal charge

0

Molecular weight

887.64 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(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)c4ccccc4O
SMILES CACTVS 3.370 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)NCCSC(=O)c4ccccc4O
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(=O)c4ccccc4O)O
Canonical SMILES CACTVS 3.370 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)NCCSC(=O)c4ccccc4O
Canonical SMILES OpenEye OEToolkits 1.7.6 CC(C)(COP(=O)(O)OP(=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)NCCSC(=O)c4ccccc4O)O

IUPAC InChI

InChI=1S/C28H40N7O18P3S/c1-28(2,22(39)25(40)31-8-7-18(37)30-9-10-57-27(41)15-5-3-4-6-16(15)36)12-50-56(47,48)53-55(45,46)49-11-17-21(52-54(42,43)44)20(38)26(51-17)35-14-34-19-23(29)32-13-33-24(19)35/h3-6,13-14,17,20-22,26,36,38-39H,7-12H2,1-2H3,(H,30,37)(H,31,40)(H,45,46)(H,47,48)(H2,29,32,33)(H2,42,43,44)/t17-,20-,21-,22+,26-/m1/s1

IUPAC InChI key

YTKKDFTVSNSVEE-TYHXJLICSA-N
2NE

wwPDB Information

Atom count

97 (57 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-12-20

Last modified at

2013-05-03

Status

Released

Obsoleted

Not Assigned



2NE : Atoms of Molecule

Total Number of Atoms: 97
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C01 N N N 0 1.34 4.51 -2.355
2 C02 C C02 N N N 0 0.916 5.769 -1.595
3 C03 C C03 N N N 0 -0.226 6.457 -2.346
4 C04 C C04 N N N 0 0.444 5.383 -0.192
5 O05 O O05 N N N 0 -0.667 4.49 -0.292
6 P06 P P06 N N N 0 -1.419 3.878 0.994
7 O07 O O07 N N N 0 -0.407 2.923 1.804
8 O08 O O08 N N N 0 -1.867 4.981 1.874
9 O09 O O09 N N N 0 -2.695 3.023 0.513
10 P10 P P10 N N N 0 -4.042 2.52 1.237
11 O11 O O11 N N N 0 -5.104 3.729 1.295
12 O12 O O12 N N N 0 -3.726 2.076 2.613
13 O13 O O13 N N N 0 -4.671 1.292 0.408
14 C14 C C14 N N N 0 -5.814 0.557 0.852
15 C15 C C15 R N N 0 -6.144 -0.535 -0.167
16 O16 O O16 N N N 0 -5.095 -1.517 -0.188
17 C17 C C17 R N N 0 -5.717 -2.794 -0.448
18 C18 C C18 R N N 0 -7.016 -2.741 0.395
19 O19 O O19 N N N 0 -8.011 -3.614 -0.145
20 C20 C C20 S N N 0 -7.443 -1.257 0.242
21 O21 O O21 N N N 0 -8.436 -1.125 -0.777
22 P22 P P22 N N N 0 -9.896 -0.505 -0.504
23 O23 O O23 N N N 0 -10.548 -1.247 0.599
24 O24 O O24 N N N 0 -9.754 1.046 -0.097
25 O25 O O25 N N N 0 -10.791 -0.631 -1.837
26 N26 N N26 N Y N 0 -4.854 -3.889 0.002
27 C27 C C27 N Y N 0 -3.883 -3.812 0.956
28 N28 N N28 N Y N 0 -3.313 -4.972 1.105
29 C29 C C29 N Y N 0 -3.881 -5.866 0.26
30 C30 C C30 N Y N 0 -3.686 -7.23 -0.012
31 N31 N N31 N N N 0 -2.717 -7.955 0.66
32 N32 N N32 N Y N 0 -4.453 -7.809 -0.93
33 C33 C C33 N Y N 0 -5.38 -7.126 -1.576
34 N34 N N34 N Y N 0 -5.598 -5.846 -1.354
35 C35 C C35 N Y N 0 -4.88 -5.183 -0.454
36 C36 C C36 R N N 0 2.105 6.726 -1.488
37 O37 O O37 N N N 0 1.677 7.954 -0.898
38 C38 C C38 N N N 0 3.176 6.102 -0.629
39 O39 O O39 N N N 0 3.432 6.575 0.458
40 N40 N N40 N N N 0 3.848 5.02 -1.069
41 C41 C C41 N N N 0 4.819 4.356 -0.197
42 C42 C C42 N N N 0 5.435 3.165 -0.933
43 C43 C C43 N N N 0 6.435 2.482 -0.035
44 O44 O O44 N N N 0 6.634 2.906 1.083
45 N45 N N45 N N N 0 7.107 1.4 -0.476
46 C46 C C46 N N N 0 8.078 0.735 0.397
47 C47 C C47 N N N 0 8.694 -0.456 -0.339
48 S48 S S48 N N N 0 9.895 -1.276 0.739
49 C49 C C49 N N N 0 10.432 -2.569 -0.33
50 O50 O O50 N N N 0 9.965 -2.668 -1.449
51 C51 C C51 N Y N 0 11.449 -3.534 0.132
52 C52 C C52 N Y N 0 11.879 -4.564 -0.715
53 O53 O O53 N N N 0 11.363 -4.68 -1.964
54 C54 C C54 N Y N 0 12.835 -5.465 -0.27
55 C55 C C55 N Y N 0 13.359 -5.346 1.002
56 C56 C C56 N Y N 0 12.937 -4.329 1.842
57 C57 C C57 N Y N 0 11.992 -3.422 1.414
58 H1 H H1 N N N 0 0.468 3.881 -2.531
59 H2 H H2 N N N 0 1.782 4.794 -3.31
60 H3 H H3 N N N 0 2.073 3.96 -1.765
61 H4 H H4 N N N 0 -1.094 5.799 -2.369
62 H5 H H5 N N N 0 -0.487 7.385 -1.837
63 H6 H H6 N N N 0 0.091 6.678 -3.365
64 H7 H H7 N N N 0 1.258 4.893 0.343
65 H8 H H8 N N N 0 0.142 6.28 0.349
66 H9 H H9 N N N 0 -0.073 2.177 1.287
67 H10 H H10 N N N 0 -5.358 4.071 0.426
68 H11 H H11 N N N 0 -5.599 0.101 1.818
69 H12 H H12 N N N 0 -6.664 1.232 0.949
70 H13 H H13 N N N 0 -6.261 -0.096 -1.157
71 H14 H H14 N N N 0 -5.951 -2.899 -1.507
72 H15 H H15 N N N 0 -6.813 -2.983 1.439
73 H16 H H16 N N N 0 -7.752 -4.546 -0.154
74 H17 H H17 N N N 0 -7.814 -0.867 1.19
75 H18 H H18 N N N 0 -9.334 1.593 -0.774
76 H19 H H19 N N N 0 -11.686 -0.276 -1.744
77 H20 H H20 N N N 0 -3.625 -2.919 1.506
78 H21 H H21 N N N 0 -2.163 -7.521 1.328
79 H22 H H22 N N N 0 -2.592 -8.896 0.463
80 H23 H H23 N N N 0 -5.982 -7.635 -2.314
81 H24 H H24 N N N 0 2.506 6.92 -2.483
82 H25 H H25 N N N 0 1.309 7.857 -0.009
83 H26 H H26 N N N 0 3.688 4.681 -1.964
84 H27 H H27 N N N 0 5.604 5.061 0.075
85 H28 H H28 N N N 0 4.317 4.005 0.705
86 H29 H H29 N N N 0 4.65 2.46 -1.205
87 H30 H H30 N N N 0 5.937 3.515 -1.835
88 H31 H H31 N N N 0 6.947 1.06 -1.37
89 H32 H H32 N N N 0 8.863 1.441 0.669
90 H33 H H33 N N N 0 7.576 0.385 1.299
91 H34 H H34 N N N 0 7.909 -1.161 -0.611
92 H35 H H35 N N N 0 9.196 -0.105 -1.241
93 H36 H H36 N N N 0 11.853 -4.189 -2.639
94 H37 H H37 N N N 0 13.17 -6.26 -0.92
95 H38 H H38 N N N 0 14.1 -6.053 1.345
96 H39 H H39 N N N 0 13.353 -4.245 2.835
97 H40 H H40 N N N 0 11.665 -2.63 2.072



2NE : Chemical Bonds

Total Number of Bonds: 100
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C55 C56 C C doub 1.38 N Y
2 C55 C54 C C sing 1.38 N Y
3 C56 C57 C C sing 1.38 N Y
4 C54 C52 C C doub 1.39 N Y
5 C57 C51 C C doub 1.4 N Y
6 C52 C51 C C sing 1.4 N Y
7 C52 O53 C O sing 1.36 N N
8 C51 C49 C C sing 1.48 N N
9 C49 S48 C S sing 1.76 N N
10 C49 O50 C O doub 1.22 N N
11 S48 C47 S C sing 1.81 N N
12 C47 C46 C C sing 1.53 N N
13 C46 N45 C N sing 1.47 N N
14 N32 C33 N C doub 1.32 N Y
15 N32 C30 N C sing 1.33 N Y
16 C33 N34 C N sing 1.32 N Y
17 N45 C43 N C sing 1.35 N N
18 N31 C30 N C sing 1.38 N N
19 C30 C29 C C doub 1.4 N Y
20 N34 C35 N C doub 1.33 N Y
21 C43 O44 C O doub 1.21 N N
22 C43 C42 C C sing 1.51 N N
23 C29 C35 C C sing 1.41 N Y
24 C29 N28 C N sing 1.35 N Y
25 C35 N26 C N sing 1.37 N Y
26 C42 C41 C C sing 1.53 N N
27 N28 C27 N C doub 1.3 N Y
28 C41 N40 C N sing 1.46 N N
29 N26 C27 N C sing 1.36 N Y
30 N26 C17 N C sing 1.47 N N
31 C17 O16 C O sing 1.44 N N
32 C17 C18 C C sing 1.55 N N
33 O19 C18 O C sing 1.43 N N
34 N40 C38 N C sing 1.35 N N
35 O23 P22 O P doub 1.48 N N
36 O16 C15 O C sing 1.44 N N
37 C18 C20 C C sing 1.55 N N
38 O21 P22 O P sing 1.61 N N
39 O21 C20 O C sing 1.43 N N
40 P22 O24 P O sing 1.61 N N
41 P22 O25 P O sing 1.61 N N
42 C20 C15 C C sing 1.54 N N
43 C38 O39 C O doub 1.21 N N
44 C38 C36 C C sing 1.51 N N
45 C15 C14 C C sing 1.53 N N
46 C03 C02 C C sing 1.53 N N
47 O37 C36 O C sing 1.43 N N
48 C36 C02 C C sing 1.53 N N
49 C14 O13 C O sing 1.43 N N
50 O13 P10 O P sing 1.61 N N
51 C02 C01 C C sing 1.53 N N
52 C02 C04 C C sing 1.53 N N
53 O12 P10 O P doub 1.48 N N
54 C04 O05 C O sing 1.43 N N
55 P10 O09 P O sing 1.61 N N
56 P10 O11 P O sing 1.61 N N
57 O09 P06 O P sing 1.61 N N
58 O05 P06 O P sing 1.61 N N
59 P06 O08 P O doub 1.48 N N
60 P06 O07 P O sing 1.61 N N
61 C01 H1 C H sing 1.09 N N
62 C01 H2 C H sing 1.09 N N
63 C01 H3 C H sing 1.09 N N
64 C03 H4 C H sing 1.09 N N
65 C03 H5 C H sing 1.09 N N
66 C03 H6 C H sing 1.09 N N
67 C04 H7 C H sing 1.09 N N
68 C04 H8 C H sing 1.09 N N
69 O07 H9 O H sing 0.97 N N
70 O11 H10 O H sing 0.97 N N
71 C14 H11 C H sing 1.09 N N
72 C14 H12 C H sing 1.09 N N
73 C15 H13 C H sing 1.09 N N
74 C17 H14 C H sing 1.09 N N
75 C18 H15 C H sing 1.09 N N
76 O19 H16 O H sing 0.97 N N
77 C20 H17 C H sing 1.09 N N
78 O24 H18 O H sing 0.97 N N
79 O25 H19 O H sing 0.97 N N
80 C27 H20 C H sing 1.08 N N
81 N31 H21 N H sing 0.97 N N
82 N31 H22 N H sing 0.97 N N
83 C33 H23 C H sing 1.08 N N
84 C36 H24 C H sing 1.09 N N
85 O37 H25 O H sing 0.97 N N
86 N40 H26 N H sing 0.97 N N
87 C41 H27 C H sing 1.09 N N
88 C41 H28 C H sing 1.09 N N
89 C42 H29 C H sing 1.09 N N
90 C42 H30 C H sing 1.09 N N
91 N45 H31 N H sing 0.97 N N
92 C46 H32 C H sing 1.09 N N
93 C46 H33 C H sing 1.09 N N
94 C47 H34 C H sing 1.09 N N
95 C47 H35 C H sing 1.09 N N
96 O53 H36 O H sing 0.97 N N
97 C54 H37 C H sing 1.08 N N
98 C55 H38 C H sing 1.08 N N
99 C56 H39 C H sing 1.08 N N
100 C57 H40 C H sing 1.08 N N



2NE : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
2NE 4i4z Open in New Window Bound ligand 9 1
2NE 4qii Open in New Window Bound ligand 12 1