Chemical Components in the PDB

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TC6 : Summary

Code

TC6

One-letter code

X

Molecule name

(2E)-Hexenoyl-CoA

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.7.2 [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-2-[[[[(3R)-4-[[3-[2-[(E)-hex-2-enoyl]sulfanylethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butoxy]-oxidanidyl-phosphoryl]oxy-oxidanidyl-phosphoryl]oxymethyl]-4-oxidanyl-oxolan-3-yl] phosphate

Formula

C27 H40 N7 O17 P3 S

Formal charge

-4

Molecular weight

859.629 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.370 CCCC=CC(=O)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
SMILES OpenEye OEToolkits 1.7.2 CCCC=CC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)([O-])OP(=O)([O-])OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)([O-])[O-])O
Canonical SMILES CACTVS 3.370 CCC/C=C/C(=O)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
Canonical SMILES OpenEye OEToolkits 1.7.2 CCC/C=C/C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)([O-])OP(=O)([O-])OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)([O-])[O-])O

IUPAC InChI

InChI=1S/C27H44N7O17P3S/c1-4-5-6-7-18(36)55-11-10-29-17(35)8-9-30-25(39)22(38)27(2,3)13-48-54(45,46)51-53(43,44)47-12-16-21(50-52(40,41)42)20(37)26(49-16)34-15-33-19-23(28)31-14-32-24(19)34/h6-7,14-16,20-22,26,37-38H,4-5,8-13H2,1-3H3,(H,29,35)(H,30,39)(H,43,44)(H,45,46)(H2,28,31,32)(H2,40,41,42)/p-4/b7-6+/t16-,20-,21-,22+,26-/m1/s1

IUPAC InChI key

OINXHIBNZUUIMR-IXUYQXAASA-J
TC6

wwPDB Information

Atom count

95 (55 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-07-29

Last modified at

2012-08-03

Status

Released

Obsoleted

Not Assigned



TC6 : Atoms of Molecule

Total Number of Atoms: 95
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 12.764 2.08 0.091
2 O1 O O1 N N N 0 12.393 2.06 -1.068
3 C2 C C2 N N N 0 13.946 2.867 0.472
4 C3 C C3 N N N 0 14.611 3.557 -0.449
5 C4 C C4 N N N 0 15.823 4.364 -0.059
6 C5 C C5 N N N 0 17.016 3.939 -0.917
7 C6 C C6 N N N 0 18.246 4.758 -0.521
8 N1A N N1A N Y N 0 -4.721 7.663 -0.175
9 O1A O O1A N N N 0 -5.014 -2.615 -2.473
10 P1A P P1A N N N 0 -5.044 -2.892 -0.954
11 C1B C C1B R N N 0 -6.088 2.682 0.375
12 S1P S S1P N N N 0 11.879 1.171 1.314
13 C2A C C2A N Y N 0 -5.528 7.122 0.719
14 O2A O O2A N N N -1 -6.1 -3.977 -0.649
15 P2A P P2A N N N 0 -2.493 -4.394 -1.104
16 C2B C C2B R N N 0 -7.544 2.619 -0.153
17 O2B O O2B N N N 0 -8.358 3.61 0.478
18 C2P C C2P N N N 0 10.578 0.445 0.286
19 N3A N N3A N Y N 0 -5.792 5.833 0.746
20 O3A O O3A N N N 0 -3.595 -3.404 -0.473
21 C3B C C3B S N N 0 -7.98 1.195 0.269
22 O3B O O3B N N N 0 -8.724 1.24 1.488
23 P3B P P3B N N N 0 -10.232 0.689 1.616
24 C3P C C3P N N N 0 9.658 -0.413 1.157
25 C4A C C4A N Y N 0 -5.243 5.011 -0.144
26 O4A O O4A N N N -1 -2.965 -5.857 -0.948
27 C4B C C4B R N N 0 -6.653 0.439 0.475
28 O4B O O4B N N N 0 -5.589 1.347 0.146
29 N4P N N4P N N N 0 8.605 -1.0 0.325
30 C5A C C5A N Y N 0 -4.377 5.538 -1.116
31 O5A O O5A N N N 0 -2.306 -4.069 -2.602
32 C5B C C5B N N N 0 -6.601 -0.78 -0.448
33 O5B O O5B N N N 0 -5.422 -1.539 -0.168
34 C5P C C5P N N N 0 7.674 -1.8 0.882
35 O5P O O5P N N N 0 7.707 -2.032 2.071
36 C6A C C6A N Y N 0 -4.127 6.92 -1.104
37 N6A N N6A N N N 0 -3.283 7.496 -2.037
38 O6A O O6A N N N 0 -1.092 -4.198 -0.334
39 C6P C C6P N N N 0 6.59 -2.404 0.025
40 N7A N N7A N Y N 0 -3.963 4.502 -1.885
41 O7A O O7A N N N -1 -10.242 -0.861 1.387
42 C7P C C7P N N N 0 5.671 -3.262 0.897
43 C8A C C8A N Y N 0 -4.508 3.4 -1.457
44 O8A O O8A N N N -1 -10.785 1.009 3.046
45 N8P N N8P N N N 0 4.618 -3.849 0.065
46 N9A N N9A N Y N 0 -5.306 3.662 -0.384
47 O9A O O9A N N N 0 -11.135 1.382 0.539
48 C9P C C9P N N N 0 3.686 -4.648 0.621
49 O9P O O9P N N N 0 3.772 -4.957 1.791
50 CAP C CAP R N N 0 2.538 -5.159 -0.21
51 OAP O OAP N N N 0 2.795 -4.896 -1.591
52 CBP C CBP N N N 0 1.248 -4.451 0.212
53 CCP C CCP N N N 0 0.112 -4.859 -0.728
54 CDP C CDP N N N 0 0.893 -4.852 1.645
55 CEP C CEP N N N 0 1.451 -2.937 0.141
56 H2 H H2 N N N 0 14.275 2.884 1.501
57 H3 H H3 N N N 0 14.283 3.54 -1.478
58 H4 H H4 N N N 0 15.62 5.423 -0.216
59 H4A H H4A N N N 0 16.052 4.189 0.993
60 H5 H H5 N N N 0 17.219 2.88 -0.76
61 H5A H H5A N N N 0 16.787 4.114 -1.969
62 H6 H H6 N N N 0 18.044 5.818 -0.678
63 H6A H H6A N N N 0 18.475 4.584 0.531
64 H6B H H6B N N N 0 19.096 4.456 -1.133
65 H1B H H1B N N N 0 -6.075 2.92 1.439
66 H2A H H2A N N N 0 -5.99 7.762 1.457
67 H2B H H2B N N N 0 -7.57 2.729 -1.237
68 HO2B H HO2B N N N 0 -8.069 4.518 0.316
69 H2P H H2P N N N 0 9.997 1.241 -0.181
70 H2PA H H2PA N N N 0 11.03 -0.176 -0.487
71 H3B H H3B N N N 0 -8.57 0.727 -0.52
72 H3P H H3P N N N 0 10.239 -1.209 1.624
73 H3PA H H3PA N N N 0 9.206 0.208 1.93
74 H4B H H4B N N N 0 -6.564 0.123 1.515
75 HN4P H HN4P N N N 0 8.579 -0.814 -0.627
76 H5B H H5B N N N 0 -7.481 -1.401 -0.28
77 H5BA H H5BA N N N 0 -6.582 -0.45 -1.486
78 HN6A H HN6A N N N 0 -3.119 8.452 -2.019
79 HN6B H HN6B N N N 0 -2.855 6.943 -2.71
80 H6P H H6P N N N 0 6.01 -1.608 -0.441
81 H6PA H H6PA N N N 0 7.042 -3.025 -0.748
82 H7P H H7P N N N 0 6.251 -4.058 1.364
83 H7PA H H7PA N N N 0 5.219 -2.641 1.67
84 H8A H H8A N N N 0 -4.35 2.423 -1.888
85 HN8P H HN8P N N N 0 4.591 -3.663 -0.887
86 HAP H HAP N N N 0 2.429 -6.233 -0.059
87 HOAP H HOAP N N N 0 2.903 -3.958 -1.799
88 HCP H HCP N N N 0 -0.032 -5.938 -0.677
89 HCPA H HCPA N N N 0 0.365 -4.574 -1.749
90 HDP H HDP N N N 0 1.666 -4.493 2.325
91 HDPA H HDPA N N N 0 -0.065 -4.41 1.919
92 HDPB H HDPB N N N 0 0.825 -5.937 1.713
93 HEP H HEP N N N 0 1.705 -2.652 -0.88
94 HEPA H HEPA N N N 0 0.533 -2.432 0.441
95 HEPB H HEPB N N N 0 2.261 -2.647 0.81



TC6 : Chemical Bonds

Total Number of Bonds: 97
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 O1 C O doub 1.22 N N
2 C1 C2 C C sing 1.47 N N
3 C1 S1P C S sing 1.76 N N
4 C2 C3 C C doub 1.33 E N
5 C3 C4 C C sing 1.51 N N
6 C4 C5 C C sing 1.53 N N
7 C5 C6 C C sing 1.53 N N
8 N1A C2A N C doub 1.32 N Y
9 N1A C6A N C sing 1.33 N Y
10 O1A P1A O P doub 1.54 N N
11 P1A O2A P O sing 1.54 N N
12 P1A O3A P O sing 1.61 N N
13 P1A O5B P O sing 1.61 N N
14 C1B C2B C C sing 1.55 N N
15 C1B O4B C O sing 1.44 N N
16 C1B N9A C N sing 1.47 N N
17 S1P C2P S C sing 1.81 N N
18 C2A N3A C N sing 1.32 N Y
19 P2A O3A P O sing 1.61 N N
20 P2A O4A P O sing 1.55 N N
21 P2A O5A P O doub 1.54 N N
22 P2A O6A P O sing 1.61 N N
23 C2B O2B C O sing 1.43 N N
24 C2B C3B C C sing 1.55 N N
25 C2P C3P C C sing 1.53 N N
26 N3A C4A N C doub 1.33 N Y
27 C3B O3B C O sing 1.43 N N
28 C3B C4B C C sing 1.54 N N
29 O3B P3B O P sing 1.61 N N
30 P3B O7A P O sing 1.57 N N
31 P3B O8A P O sing 1.57 N N
32 P3B O9A P O doub 1.57 N N
33 C3P N4P C N sing 1.46 N N
34 C4A C5A C C sing 1.4 N Y
35 C4A N9A C N sing 1.37 N Y
36 C4B O4B C O sing 1.44 N N
37 C4B C5B C C sing 1.53 N N
38 N4P C5P N C sing 1.35 N N
39 C5A C6A C C doub 1.4 N Y
40 C5A N7A C N sing 1.36 N Y
41 C5B O5B C O sing 1.43 N N
42 C5P O5P C O doub 1.21 N N
43 C5P C6P C C sing 1.51 N N
44 C6A N6A C N sing 1.38 N N
45 O6A CCP O C sing 1.43 N N
46 C6P C7P C C sing 1.53 N N
47 N7A C8A N C doub 1.3 N Y
48 C7P N8P C N sing 1.46 N N
49 C8A N9A C N sing 1.36 N Y
50 N8P C9P N C sing 1.35 N N
51 C9P O9P C O doub 1.21 N N
52 C9P CAP C C sing 1.51 N N
53 CAP OAP C O sing 1.43 N N
54 CAP CBP C C sing 1.53 N N
55 CBP CCP C C sing 1.53 N N
56 CBP CDP C C sing 1.53 N N
57 CBP CEP C C sing 1.53 N N
58 C2 H2 C H sing 1.08 N N
59 C3 H3 C H sing 1.08 N N
60 C4 H4 C H sing 1.09 N N
61 C4 H4A C H sing 1.09 N N
62 C5 H5 C H sing 1.09 N N
63 C5 H5A C H sing 1.09 N N
64 C6 H6 C H sing 1.09 N N
65 C6 H6A C H sing 1.09 N N
66 C6 H6B C H sing 1.09 N N
67 C1B H1B C H sing 1.09 N N
68 C2A H2A C H sing 1.08 N N
69 C2B H2B C H sing 1.09 N N
70 O2B HO2B O H sing 0.97 N N
71 C2P H2P C H sing 1.09 N N
72 C2P H2PA C H sing 1.09 N N
73 C3B H3B C H sing 1.09 N N
74 C3P H3P C H sing 1.09 N N
75 C3P H3PA C H sing 1.09 N N
76 C4B H4B C H sing 1.09 N N
77 N4P HN4P N H sing 0.97 N N
78 C5B H5B C H sing 1.09 N N
79 C5B H5BA C H sing 1.09 N N
80 N6A HN6A N H sing 0.97 N N
81 N6A HN6B N H sing 0.97 N N
82 C6P H6P C H sing 1.09 N N
83 C6P H6PA C H sing 1.09 N N
84 C7P H7P C H sing 1.09 N N
85 C7P H7PA C H sing 1.09 N N
86 C8A H8A C H sing 1.08 N N
87 N8P HN8P N H sing 0.97 N N
88 CAP HAP C H sing 1.09 N N
89 OAP HOAP O H sing 0.97 N N
90 CCP HCP C H sing 1.09 N N
91 CCP HCPA C H sing 1.09 N N
92 CDP HDP C H sing 1.09 N N
93 CDP HDPA C H sing 1.09 N N
94 CDP HDPB C H sing 1.09 N N
95 CEP HEP C H sing 1.09 N N
96 CEP HEPA C H sing 1.09 N N
97 CEP HEPB C H sing 1.09 N N



TC6 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
TC6 3zwb Open in New Window Bound ligand 2 1