Chemical Components in the PDB

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2MC : Summary

Code

2MC

One-letter code

X

Molecule name

METHACRYLYL-COENZYME A

Systematic names

ProgramVersionName
ACDLabs 10.04 S-{(9R,13S,15R)-17-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-9,13,15-trihydroxy-10,10-dimethyl-13,15-dioxido-4,8-dioxo-12,14,16-trioxa-3,7-diaza-13,15-diphosphaheptadec-1-yl} 2-methylprop-2-enethioate (non-preferred name)
OpenEye OEToolkits 1.5.0 S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-2-hydroxy-3,3-dimethyl-butanoyl]amino]propanoylamino]ethyl] 2-methylprop-2-enethioate

Formula

C25 H40 N7 O17 P3 S

Formal charge

0

Molecular weight

835.608 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 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)\C(=C)C
SMILES CACTVS 3.385 CC(=C)C(=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 1.7.5 CC(=C)C(=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 3.385 CC(=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 1.7.5 CC(=C)C(=O)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

IUPAC InChI

InChI=1S/C25H40N7O17P3S/c1-13(2)24(37)53-8-7-27-15(33)5-6-28-22(36)19(35)25(3,4)10-46-52(43,44)49-51(41,42)45-9-14-18(48-50(38,39)40)17(34)23(47-14)32-12-31-16-20(26)29-11-30-21(16)32/h11-12,14,17-19,23,34-35H,1,5-10H2,2-4H3,(H,27,33)(H,28,36)(H,41,42)(H,43,44)(H2,26,29,30)(H2,38,39,40)/t14-,17-,18-,19+,23-/m1/s1

IUPAC InChI key

NPALUEYCDZWBOV-NDZSKPAWSA-N
2MC

wwPDB Information

Atom count

93 (53 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2004-01-19

Last modified at

2012-01-05

Status

Released

Obsoleted

Not Assigned



2MC : Atoms of Molecule

Total Number of Atoms: 93
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1A N AN1 N Y N 0 -7.557 6.672 1.826
2 C2A C AC2 N Y N 0 -8.131 5.539 2.187
3 N3A N AN3 N Y N 0 -7.693 4.365 1.783
4 C4A C AC4 N Y N 0 -6.636 4.276 0.981
5 C5A C AC5 N Y N 0 -5.99 5.454 0.568
6 C6A C AC6 N Y N 0 -6.496 6.682 1.026
7 N6A N AN6 N N N 0 -5.902 7.875 0.653
8 N7A N AN7 N Y N 0 -4.96 5.085 -0.23
9 C8A C AC8 N Y N 0 -4.933 3.788 -0.332
10 N9A N AN9 N Y N 0 -5.947 3.243 0.398
11 C1B C AC1* R N N 0 -6.247 1.815 0.534
12 C2B C AC2* R N N 0 -7.324 1.383 -0.492
13 O2B O AO2* N N N 0 -8.638 1.606 0.023
14 C3B C AC3* S N N 0 -7.04 -0.132 -0.642
15 O3B O AO3* N N N 0 -7.926 -0.891 0.182
16 P3B P AP3* N N N 0 -8.926 -2.009 -0.403
17 O7A O AO7 N N N 0 -8.154 -3.001 -1.184
18 O8A O AO8 N N N 0 -9.674 -2.75 0.815
19 O9A O AO9 N N N 0 -10.018 -1.308 -1.356
20 C4B C AC4* R N N 0 -5.585 -0.292 -0.161
21 O4B O AO4* N N N 0 -5.098 1.018 0.173
22 C5B C AC5* N N N 0 -4.731 -0.896 -1.278
23 O5B O AO5* N N N 0 -3.413 -1.149 -0.786
24 P1A P AP1 R N N 0 -2.246 -1.785 -1.694
25 O1A O AO1 N N N 0 -2.712 -3.065 -2.273
26 O2A O AO2 N N N 0 -1.873 -0.763 -2.881
27 O3A O AO3 N N N 0 -0.943 -2.05 -0.785
28 P2A P AP2 S N N 0 0.402 -2.912 -0.983
29 O4A O AO4 N N N 0 0.072 -4.197 -1.64
30 O5A O AO5 N N N 0 1.437 -2.09 -1.902
31 O6A O AO6 N N N 0 1.07 -3.2 0.453
32 CBP C PC11 N N N 0 2.592 -4.09 2.107
33 CCP C PC12 N N N 0 2.221 -4.03 0.623
34 CDP C PC13 N N N 0 2.901 -2.679 2.612
35 CEP C PC14 N N N 0 1.421 -4.671 2.902
36 CAP C PC10 R N N 0 3.823 -4.979 2.289
37 OAP O PO10 N N N 0 3.494 -6.326 1.943
38 C9P C PC9 N N N 0 4.934 -4.488 1.397
39 O9P O PO9 N N N 0 5.297 -5.16 0.455
40 N8P N PN8 N N N 0 5.524 -3.302 1.646
41 C7P C PC7 N N N 0 6.536 -2.779 0.724
42 C6P C PC6 N N N 0 7.041 -1.428 1.235
43 C5P C PC5 N N N 0 8.082 -0.891 0.287
44 O5P O PO5 N N N 0 8.389 -1.525 -0.7
45 N4P N PN4 N N N 0 8.672 0.296 0.535
46 C3P C PC3 N N N 0 9.684 0.818 -0.386
47 C2P C PC2 N N N 0 10.189 2.169 0.124
48 S1P S PS1 N N N 0 11.439 2.815 -1.014
49 C1 C C1 N N N 0 11.835 4.33 -0.207
50 O2 O O2 N N N 0 11.275 4.631 0.83
51 C2 C C2 N N N 0 12.843 5.231 -0.786
52 C3 C C3 N N N 0 13.142 6.374 -0.177
53 C2M C C2M N N N 0 13.538 4.857 -2.071
54 H2 H H2 N N N 0 -8.991 5.576 2.838
55 HN61 H 1HN6 N N N 0 -6.26 8.717 0.975
56 HN62 H 2HN6 N N N 0 -5.127 7.87 0.069
57 H8 H H8 N N N 0 -4.214 3.227 -0.909
58 H1' H H1* N N N 0 -6.57 1.587 1.55
59 H2' H H2* N N N 0 -7.187 1.901 -1.441
60 H3 H H3 N N N 0 -8.832 2.533 0.219
61 H3' H H3* N N N 0 -7.135 -0.436 -1.685
62 HO8 H HO8 N N N 0 -10.294 -3.438 0.535
63 HO9 H HO9 N N N 0 -10.561 -0.644 -0.909
64 HO2 H HO2 N N N 0 -1.559 0.099 -2.575
65 H4' H H4* N N N 0 -5.555 -0.934 0.72
66 H5'1 H 1H5* N N N 0 -5.18 -1.831 -1.613
67 H5'2 H 2H5* N N N 0 -4.679 -0.198 -2.113
68 HO5 H HO5 N N N 0 1.697 -1.235 -1.532
69 H121 H 1H12 N N N 0 2.0 -5.035 0.264
70 H122 H 2H12 N N N 0 3.055 -3.616 0.057
71 H131 H 1H13 N N N 0 1.993 -2.077 2.588
72 H132 H 2H13 N N N 0 3.275 -2.734 3.635
73 H133 H 3H13 N N N 0 3.657 -2.222 1.973
74 H141 H 1H14 N N N 0 1.24 -5.698 2.584
75 H142 H 2H14 N N N 0 1.662 -4.657 3.965
76 H143 H 3H14 N N N 0 0.528 -4.072 2.724
77 H1 H H1 N N N 0 4.149 -4.94 3.329
78 H10 H H10 N N N 0 3.196 -6.435 1.029
79 HN8 H HN8 N N N 0 5.278 -2.794 2.435
80 H71 H 1H7 N N N 0 7.369 -3.48 0.664
81 H72 H 2H7 N N N 0 6.095 -2.652 -0.265
82 H61 H 1H6 N N N 0 6.208 -0.728 1.295
83 H62 H 2H6 N N N 0 7.482 -1.555 2.224
84 HN4 H HN4 N N N 0 8.426 0.803 1.324
85 H31 H 1H3 N N N 0 10.516 0.118 -0.447
86 H32 H 2H3 N N N 0 9.243 0.945 -1.375
87 H21 H 1H2 N N N 0 9.356 2.869 0.184
88 H22 H 2H2 N N N 0 10.63 2.042 1.113
89 H12 H 2H1 N N N 0 12.645 6.641 0.743
90 H11 H 1H1 N N N 0 13.882 7.035 -0.603
91 H2M1 H 1H2M N N N 0 13.165 3.894 -2.419
92 H2M2 H 2H2M N N N 0 13.339 5.618 -2.826
93 H2M3 H 3H2M N N N 0 14.612 4.79 -1.897



2MC : Chemical Bonds

Total Number of Bonds: 95
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1A C2A N C doub 1.32 N Y
2 N1A C6A N C sing 1.33 N Y
3 C2A N3A C N sing 1.32 N Y
4 C2A H2 C H sing 1.08 N N
5 N3A C4A N C doub 1.33 N Y
6 C4A C5A C C sing 1.41 N Y
7 C4A N9A C N sing 1.37 N Y
8 C5A C6A C C doub 1.4 N Y
9 C5A N7A C N sing 1.35 N Y
10 C6A N6A C N sing 1.38 N N
11 N6A HN61 N H sing 0.97 N N
12 N6A HN62 N H sing 0.97 N N
13 N7A C8A N C doub 1.3 N Y
14 C8A N9A C N sing 1.36 N Y
15 C8A H8 C H sing 1.08 N N
16 N9A C1B N C sing 1.47 N N
17 C1B C2B C C sing 1.55 N N
18 C1B O4B C O sing 1.44 N N
19 C1B H1' C H sing 1.09 N N
20 C2B O2B C O sing 1.43 N N
21 C2B C3B C C sing 1.55 N N
22 C2B H2' C H sing 1.09 N N
23 O2B H3 O H sing 0.97 N N
24 C3B O3B C O sing 1.43 N N
25 C3B C4B C C sing 1.54 N N
26 C3B H3' C H sing 1.09 N N
27 O3B P3B O P sing 1.61 N N
28 P3B O7A P O doub 1.48 N N
29 P3B O8A P O sing 1.61 N N
30 P3B O9A P O sing 1.61 N N
31 O8A HO8 O H sing 0.97 N N
32 O9A HO9 O H sing 0.97 N N
33 C4B O4B C O sing 1.44 N N
34 C4B C5B C C sing 1.53 N N
35 C4B H4' C H sing 1.09 N N
36 C5B O5B C O sing 1.43 N N
37 C5B H5'1 C H sing 1.09 N N
38 C5B H5'2 C H sing 1.09 N N
39 O5B P1A O P sing 1.61 N N
40 P1A O1A P O doub 1.48 N N
41 P1A O2A P O sing 1.61 N N
42 P1A O3A P O sing 1.61 N N
43 O2A HO2 O H sing 0.97 N N
44 O3A P2A O P sing 1.61 N N
45 P2A O4A P O doub 1.48 N N
46 P2A O5A P O sing 1.61 N N
47 P2A O6A P O sing 1.61 N N
48 O5A HO5 O H sing 0.97 N N
49 O6A CCP O C sing 1.43 N N
50 CBP CCP C C sing 1.53 N N
51 CBP CDP C C sing 1.53 N N
52 CBP CEP C C sing 1.53 N N
53 CBP CAP C C sing 1.53 N N
54 CCP H121 C H sing 1.09 N N
55 CCP H122 C H sing 1.09 N N
56 CDP H131 C H sing 1.09 N N
57 CDP H132 C H sing 1.09 N N
58 CDP H133 C H sing 1.09 N N
59 CEP H141 C H sing 1.09 N N
60 CEP H142 C H sing 1.09 N N
61 CEP H143 C H sing 1.09 N N
62 CAP OAP C O sing 1.43 N N
63 CAP C9P C C sing 1.51 N N
64 CAP H1 C H sing 1.09 N N
65 OAP H10 O H sing 0.97 N N
66 C9P O9P C O doub 1.21 N N
67 C9P N8P C N sing 1.35 N N
68 N8P C7P N C sing 1.47 N N
69 N8P HN8 N H sing 0.97 N N
70 C7P C6P C C sing 1.53 N N
71 C7P H71 C H sing 1.09 N N
72 C7P H72 C H sing 1.09 N N
73 C6P C5P C C sing 1.51 N N
74 C6P H61 C H sing 1.09 N N
75 C6P H62 C H sing 1.09 N N
76 C5P O5P C O doub 1.21 N N
77 C5P N4P C N sing 1.35 N N
78 N4P C3P N C sing 1.46 N N
79 N4P HN4 N H sing 0.97 N N
80 C3P C2P C C sing 1.53 N N
81 C3P H31 C H sing 1.09 N N
82 C3P H32 C H sing 1.09 N N
83 C2P S1P C S sing 1.81 N N
84 C2P H21 C H sing 1.09 N N
85 C2P H22 C H sing 1.09 N N
86 S1P C1 S C sing 1.76 N N
87 C1 O2 C O doub 1.22 N N
88 C1 C2 C C sing 1.47 N N
89 C2 C3 C C doub 1.33 N N
90 C2 C2M C C sing 1.51 N N
91 C3 H11 C H sing 1.08 N N
92 C3 H12 C H sing 1.08 N N
93 C2M H2M1 C H sing 1.09 N N
94 C2M H2M2 C H sing 1.09 N N
95 C2M H2M3 C H sing 1.09 N N



2MC : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
2MC 1rx0 Open in New Window Bound ligand 2 1