Chemical Components in the PDB

pdbe.org/chem
spacer

0RQ : Summary

Code

0RQ

One-letter code

X

Molecule name

[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3R)-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-(4-oxidanylidenepentylamino)propyl]amino]butyl] hydrogen phosphate

Synonyms

dethiaacetyl-coenzyme A

Systematic names

ProgramVersionName
ACDLabs 12.01 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-3-hydroxy-2,2-dimethyl-4-oxo-4-({3-oxo-3-[(4-oxopentyl)amino]propyl}amino)butyl dihydrogen diphosphate (non-preferred name)
OpenEye OEToolkits 1.7.6 [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3R)-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-(4-oxidanylidenepentylamino)propyl]amino]butyl] hydrogen phosphate

Formula

C24 H40 N7 O17 P3

Formal charge

0

Molecular weight

791.532 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(C)CCCNC(=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 CC(=O)CCCNC(=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 1.7.6 CC(=O)CCCNC(=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 CC(=O)CCCNC(=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 1.7.6 CC(=O)CCCNC(=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/C24H40N7O17P3/c1-13(32)5-4-7-26-15(33)6-8-27-22(36)19(35)24(2,3)10-45-51(42,43)48-50(40,41)44-9-14-18(47-49(37,38)39)17(34)23(46-14)31-12-30-16-20(25)28-11-29-21(16)31/h11-12,14,17-19,23,34-35H,4-10H2,1-3H3,(H,26,33)(H,27,36)(H,40,41)(H,42,43)(H2,25,28,29)(H2,37,38,39)/t14-,17-,18-,19+,23-/m1/s1

IUPAC InChI key

ZYXBXYCDXPIBJY-NDZSKPAWSA-N
0RQ

wwPDB Information

Atom count

91 (51 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-05-06

Last modified at

2012-10-05

Status

Released

Obsoleted

Not Assigned



0RQ : Atoms of Molecule

Total Number of Atoms: 91
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O3B O O3B N N N 0 7.13 1.391 0.263
2 O7A O O7A N N N 0 7.159 3.559 -1.03
3 O8A O O8A N N N 0 8.675 3.394 0.98
4 O9A O O9A N N N 0 9.185 2.067 -1.232
5 O4B O O4B N N N 0 4.509 -0.791 0.151
6 O5B O O5B N N N 0 2.622 1.213 -0.765
7 O1A O O1A N N N 0 1.164 0.748 -2.903
8 O2A O O2A N N N 0 1.736 3.1 -2.188
9 O3A O O3A N N N 0 0.068 1.837 -0.776
10 O4A O O4A N N N 0 -1.164 3.895 -1.564
11 O5A O O5A N N N 0 -2.285 1.664 -1.935
12 O6A O O6A N N N 0 -2.078 2.709 0.468
13 CDP C CDP N N N 0 -3.872 1.902 2.569
14 CEP C CEP N N N 0 -2.624 4.03 2.967
15 CCP C CCP N N N 0 -3.315 3.401 0.65
16 CAP C CAP R N N 0 -5.036 4.099 2.32
17 CBP C CBP N N N 0 -3.712 3.358 2.126
18 C1B C C1B R N N 0 5.728 -1.48 0.502
19 C2B C C2B R N N 0 6.767 -0.907 -0.494
20 C3B C C3B S N N 0 6.334 0.575 -0.599
21 C5B C C5B N N N 0 3.966 1.125 -1.241
22 P3B P P3B N N N 0 8.019 2.623 -0.271
23 P1A P P1A N N N 0 1.405 1.754 -1.669
24 P2A P P2A N N N 0 -1.36 2.556 -0.965
25 C2P C C2P N N N 0 -10.546 -3.605 -0.249
26 C3P C C3P N N N 0 -10.184 -2.187 -0.695
27 C7P C C7P N N N 0 -7.467 1.683 0.617
28 C6P C C6P N N N 0 -7.829 0.265 1.064
29 C5P C C5P N N N 0 -8.79 -0.343 0.075
30 C9P C C9P N N N 0 -6.073 3.527 1.388
31 C4B C C4B R N N 0 4.865 0.573 -0.132
32 OAP O OAP N N N 0 -4.852 5.487 2.034
33 O9P O O9P N N N 0 -6.494 4.194 0.467
34 O5P O O5P N N N 0 -9.151 0.295 -0.891
35 N8P N N8P N N N 0 -6.533 2.274 1.578
36 N4P N N4P N N N 0 -9.25 -1.596 0.266
37 O2B O O2B N N N 0 8.092 -1.015 0.032
38 C2A C C2A N Y N 0 7.811 -5.058 2.236
39 C6A C C6A N Y N 0 6.383 -6.316 0.93
40 C5M C C5M N Y N 0 5.808 -5.127 0.45
41 C4A C C4A N Y N 0 6.303 -3.906 0.939
42 C8A C C8A N Y N 0 4.684 -3.542 -0.512
43 N6A N N6A N N N 0 5.931 -7.548 0.492
44 N1A N N1A N Y N 0 7.372 -6.229 1.813
45 N3A N N3A N Y N 0 7.3 -3.919 1.819
46 N9A N N9A N Y N 0 5.575 -2.925 0.315
47 N7A N N7A N Y N 0 4.817 -4.833 -0.425
48 C1P C C1P N N N 0 -11.522 -4.222 -1.252
49 C C C N N N 0 -11.878 -5.619 -0.812
50 O O O N N N 0 -11.401 -6.074 0.199
51 CH3 C CH3 N N N 0 -12.831 -6.448 -1.635
52 H1 H H1 N N N 0 9.225 4.149 0.733
53 H2 H H2 N N N 0 9.788 1.447 -0.799
54 H3 H H3 N N N 0 0.942 -0.155 -2.637
55 H4 H H4 N N N 0 -2.456 0.771 -1.605
56 H5 H H5 N N N 0 -4.564 1.392 1.898
57 H6 H H6 N N N 0 -2.903 1.404 2.539
58 H7 H H7 N N N 0 -4.265 1.873 3.586
59 H8 H H8 N N N 0 -2.878 3.946 4.023
60 H9 H H9 N N N 0 -1.668 3.54 2.782
61 H10 H H10 N N N 0 -2.552 5.082 2.693
62 H11 H H11 N N N 0 -3.201 4.438 0.334
63 H12 H H12 N N N 0 -4.09 2.922 0.051
64 H13 H H13 N N N 0 -5.371 3.982 3.351
65 H14 H H14 N N N 0 6.013 -1.256 1.53
66 H15 H H15 N N N 0 6.693 -1.403 -1.462
67 H16 H H16 N N N 0 6.408 0.923 -1.629
68 H17 H H17 N N N 0 4.004 0.461 -2.104
69 H18 H H18 N N N 0 4.314 2.117 -1.53
70 H19 H H19 N N N 0 -9.642 -4.212 -0.2
71 H20 H H20 N N N 0 -11.012 -3.568 0.736
72 H21 H H21 N N N 0 -9.718 -2.224 -1.68
73 H22 H H22 N N N 0 -7.001 1.646 -0.367
74 H23 H H23 N N N 0 -8.371 2.29 0.569
75 H24 H H24 N N N 0 -6.925 -0.342 1.112
76 H25 H H25 N N N 0 -8.295 0.302 2.048
77 H26 H H26 N N N 0 4.758 1.179 0.767
78 H27 H H27 N N N 0 -4.555 5.666 1.132
79 H28 H H28 N N N 0 -6.244 1.764 2.351
80 H29 H H29 N N N 0 8.375 -1.924 0.199
81 H30 H H30 N N N 0 8.617 -5.033 2.955
82 H31 H H31 N N N 0 3.969 -3.033 -1.142
83 H32 H H32 N N N 0 6.336 -8.362 0.831
84 H33 H H33 N N N 0 5.208 -7.598 -0.153
85 H34 H H34 N N N 0 -12.426 -3.615 -1.301
86 H35 H H35 N N N 0 -11.056 -4.259 -2.237
87 H36 H H36 N N N 0 -12.269 -7.02 -2.374
88 H37 H H37 N N N 0 -13.374 -7.132 -0.983
89 H38 H H38 N N N 0 -13.537 -5.792 -2.144
90 H39 H H39 N N N 0 -11.088 -1.579 -0.744
91 H40 H H40 N N N 0 -8.962 -2.106 1.038



0RQ : Chemical Bonds

Total Number of Bonds: 93
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1P C C C sing 1.51 N N
2 C1P C2P C C sing 1.53 N N
3 CH3 C C C sing 1.51 N N
4 C O C O doub 1.21 N N
5 C2P C3P C C sing 1.53 N N
6 C3P N4P C N sing 1.46 N N
7 N4P C5P N C sing 1.35 N N
8 C5P O5P C O doub 1.21 N N
9 C5P C6P C C sing 1.51 N N
10 C6P C7P C C sing 1.53 N N
11 C7P N8P C N sing 1.46 N N
12 N8P C9P N C sing 1.35 N N
13 OAP CAP O C sing 1.43 N N
14 O4A P2A O P doub 1.48 N N
15 C9P O9P C O doub 1.21 N N
16 C9P CAP C C sing 1.51 N N
17 O5A P2A O P sing 1.61 N N
18 CAP CBP C C sing 1.53 N N
19 P2A O6A P O sing 1.61 N N
20 P2A O3A P O sing 1.61 N N
21 O6A CCP O C sing 1.43 N N
22 CBP CCP C C sing 1.53 N N
23 CBP CDP C C sing 1.53 N N
24 CBP CEP C C sing 1.53 N N
25 O3A P1A O P sing 1.61 N N
26 O2A P1A O P doub 1.48 N N
27 P1A O5B P O sing 1.61 N N
28 P1A O1A P O sing 1.61 N N
29 C5B O5B C O sing 1.43 N N
30 C5B C4B C C sing 1.53 N N
31 O7A P3B O P doub 1.48 N N
32 C4B O4B C O sing 1.44 N N
33 C4B C3B C C sing 1.54 N N
34 O4B C1B O C sing 1.44 N N
35 C3B O3B C O sing 1.43 N N
36 C3B C2B C C sing 1.55 N N
37 P3B O3B P O sing 1.61 N N
38 P3B O9A P O sing 1.61 N N
39 P3B O8A P O sing 1.61 N N
40 C2B C1B C C sing 1.55 N N
41 C2B O2B C O sing 1.43 N N
42 C1B N9A C N sing 1.47 N N
43 C8A N9A C N sing 1.36 N Y
44 C8A N7A C N doub 1.3 N Y
45 N9A C4A N C sing 1.37 N Y
46 N7A C5M N C sing 1.35 N Y
47 C4A C5M C C doub 1.41 N Y
48 C4A N3A C N sing 1.33 N Y
49 C5M C6A C C sing 1.41 N Y
50 N3A C2A N C doub 1.32 N Y
51 C6A N6A C N sing 1.38 N N
52 C6A N1A C N doub 1.33 N Y
53 C2A N1A C N sing 1.32 N Y
54 O8A H1 O H sing 0.97 N N
55 O9A H2 O H sing 0.97 N N
56 O1A H3 O H sing 0.97 N N
57 O5A H4 O H sing 0.97 N N
58 CDP H5 C H sing 1.09 N N
59 CDP H6 C H sing 1.09 N N
60 CDP H7 C H sing 1.09 N N
61 CEP H8 C H sing 1.09 N N
62 CEP H9 C H sing 1.09 N N
63 CEP H10 C H sing 1.09 N N
64 CCP H11 C H sing 1.09 N N
65 CCP H12 C H sing 1.09 N N
66 CAP H13 C H sing 1.09 N N
67 C1B H14 C H sing 1.09 N N
68 C2B H15 C H sing 1.09 N N
69 C3B H16 C H sing 1.09 N N
70 C5B H17 C H sing 1.09 N N
71 C5B H18 C H sing 1.09 N N
72 C2P H19 C H sing 1.09 N N
73 C2P H20 C H sing 1.09 N N
74 C3P H21 C H sing 1.09 N N
75 C7P H22 C H sing 1.09 N N
76 C7P H23 C H sing 1.09 N N
77 C6P H24 C H sing 1.09 N N
78 C6P H25 C H sing 1.09 N N
79 C4B H26 C H sing 1.09 N N
80 OAP H27 O H sing 0.97 N N
81 N8P H28 N H sing 0.97 N N
82 O2B H29 O H sing 0.97 N N
83 C2A H30 C H sing 1.08 N N
84 C8A H31 C H sing 1.08 N N
85 N6A H32 N H sing 0.97 N N
86 N6A H33 N H sing 0.97 N N
87 C1P H34 C H sing 1.09 N N
88 C1P H35 C H sing 1.09 N N
89 CH3 H36 C H sing 1.09 N N
90 CH3 H37 C H sing 1.09 N N
91 CH3 H38 C H sing 1.09 N N
92 C3P H39 C H sing 1.09 N N
93 N4P H40 N H sing 0.97 N N



0RQ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
0RQ 4euc Open in New Window Bound ligand 2 1