Chemical Components in the PDB

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0T1 : Summary

Code

0T1

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-(propylamino)propyl]amino]butyl] hydrogen phosphate

Synonyms

DETHIACOENZYME 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-(propylamino)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-(propylamino)propyl]amino]butyl] hydrogen phosphate

Formula

C22 H38 N7 O16 P3

Formal charge

0

Molecular weight

749.496 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NCCC)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 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 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 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 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/C22H38N7O16P3/c1-4-6-24-13(30)5-7-25-20(33)17(32)22(2,3)9-42-48(39,40)45-47(37,38)41-8-12-16(44-46(34,35)36)15(31)21(43-12)29-11-28-14-18(23)26-10-27-19(14)29/h10-12,15-17,21,31-32H,4-9H2,1-3H3,(H,24,30)(H,25,33)(H,37,38)(H,39,40)(H2,23,26,27)(H2,34,35,36)/t12-,15-,16-,17+,21-/m1/s1

IUPAC InChI key

JJSFSVFKDOGQNC-GORZOVPNSA-N
0T1

wwPDB Information

Atom count

86 (48 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-05-29

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



0T1 : Atoms of Molecule

Total Number of Atoms: 86
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1A N N1A N Y N 0 -5.389 6.165 1.728
2 C2A C C2A N Y N 0 -6.097 5.101 2.06
3 N3A N N3A N Y N 0 -5.744 3.881 1.713
4 N6A N N6A N N N 0 -3.535 7.174 0.674
5 C4A C C4A N Y N 0 -4.641 3.671 1.002
6 C5M C C5M N Y N 0 -3.853 4.771 0.623
7 C6A C C6A N Y N 0 -4.271 6.053 1.018
8 N7A N N7A N Y N 0 -2.804 4.286 -0.083
9 C8A C C8A N Y N 0 -2.896 2.99 -0.161
10 N9A N N9A N Y N 0 -4.013 2.562 0.493
11 C1B C C1B R N N 0 -4.46 1.174 0.628
12 C2B C C2B R N N 0 -5.49 0.823 -0.476
13 O2B O O2B N N N 0 -6.813 1.184 -0.073
14 C3B C C3B S N N 0 -5.345 -0.715 -0.578
15 O3B O O3B N N N 0 -6.364 -1.366 0.184
16 P3B P P3B N N N 0 -7.418 -2.396 -0.463
17 O7A O O7A N N N 0 -8.357 -1.615 -1.512
18 O8A O O8A N N N 0 -6.688 -3.476 -1.162
19 O9A O O9A N N N 0 -8.33 -3.032 0.702
20 C4B C C4B R N N 0 -3.955 -1.004 0.023
21 O4B O O4B N N N 0 -3.37 0.262 0.374
22 C5B C C5B N N N 0 -3.078 -1.713 -1.011
23 O5B O O5B N N N 0 -1.835 -2.08 -0.41
24 P1A P P1A N N N 0 -0.667 -2.847 -1.209
25 O1A O O1A N N N 0 -0.315 -2.079 -2.425
26 O2A O O2A N N N 0 -1.179 -4.314 -1.631
27 O3A O O3A N N N 0 0.631 -2.981 -0.265
28 P2A P P2A N N N 0 2.194 -3.246 -0.544
29 O4A O O4A N N N 0 2.418 -4.795 -0.919
30 O5A O O5A N N N 0 2.645 -2.396 -1.669
31 O6A O O6A N N N 0 3.043 -2.885 0.775
32 CBP C CBP N N N 0 4.952 -2.52 2.212
33 CCP C CCP N N N 0 4.471 -2.914 0.814
34 CDP C CDP N N N 0 4.462 -1.108 2.54
35 CEP C CEP N N N 0 4.393 -3.505 3.24
36 CAP C CAP R N N 0 6.481 -2.551 2.253
37 OAP O OAP N N N 0 6.934 -3.895 2.076
38 C9P C C9P N N N 0 7.031 -1.685 1.15
39 O9P O O9P N N N 0 7.611 -2.193 0.213
40 N8P N N8P N N N 0 6.879 -0.347 1.203
41 C7P C C7P N N N 0 7.327 0.486 0.085
42 C6P C C6P N N N 0 7.04 1.956 0.398
43 C5P C C5P N N N 0 7.501 2.814 -0.752
44 O5P O O5P N N N 0 8.009 2.3 -1.726
45 N4P N N4P N N N 0 7.349 4.152 -0.698
46 C3P C C3P N N N 0 7.797 4.986 -1.817
47 C2P C C2P N N N 0 7.51 6.456 -1.504
48 C1P C C1P N N N 0 7.978 7.326 -2.672
49 H1 H H1 N N N 0 -6.999 5.236 2.638
50 H2 H H2 N N N 0 -3.834 8.054 0.952
51 H3 H H3 N N N 0 -2.721 7.08 0.156
52 H4 H H4 N N N 0 -2.191 2.348 -0.669
53 H5 H H5 N N N 0 -4.885 1.003 1.617
54 H6 H H6 N N N 0 -5.228 1.302 -1.419
55 H7 H H7 N N N 0 -6.929 2.13 0.092
56 H8 H H8 N N N 0 -5.383 -1.034 -1.62
57 H9 H H9 N N N 0 -8.867 -0.892 -1.122
58 H10 H H10 N N N 0 -8.99 -3.664 0.385
59 H11 H H11 N N N 0 -4.058 -1.626 0.912
60 H12 H H12 N N N 0 -3.588 -2.608 -1.367
61 H13 H H13 N N N 0 -2.892 -1.043 -1.85
62 H14 H H14 N N N 0 -1.427 -4.874 -0.882
63 H15 H H15 N N N 0 2.144 -5.411 -0.226
64 H16 H H16 N N N 0 4.82 -3.92 0.58
65 H17 H H17 N N N 0 4.869 -2.212 0.081
66 H18 H H18 N N N 0 4.765 -0.424 1.747
67 H19 H H19 N N N 0 3.375 -1.11 2.622
68 H20 H H20 N N N 0 4.896 -0.783 3.485
69 H21 H H21 N N N 0 4.667 -3.178 4.243
70 H22 H H22 N N N 0 3.307 -3.543 3.155
71 H23 H H23 N N N 0 4.807 -4.497 3.055
72 H24 H H24 N N N 0 6.826 -2.175 3.217
73 H25 H H25 N N N 0 6.663 -4.294 1.238
74 H26 H H26 N N N 0 6.473 0.064 1.982
75 H27 H H27 N N N 0 8.398 0.349 -0.064
76 H28 H H28 N N N 0 6.794 0.197 -0.82
77 H32 H H32 N N N 0 8.868 4.848 -1.966
78 H29 H H29 N N N 0 5.969 2.094 0.547
79 H30 H H30 N N N 0 7.573 2.246 1.304
80 H31 H H31 N N N 0 6.943 4.563 0.08
81 H33 H H33 N N N 0 7.264 4.696 -2.722
82 H34 H H34 N N N 0 6.439 6.593 -1.355
83 H35 H H35 N N N 0 8.043 6.745 -0.598
84 H36 H H36 N N N 0 9.049 7.189 -2.821
85 H37 H H37 N N N 0 7.445 7.037 -3.577
86 H38 H H38 N N N 0 7.774 8.374 -2.449



0T1 : Chemical Bonds

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



0T1 : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
0T1 5dw5 Open in New Window Bound ligand 2 1
0T1 5dw6 Open in New Window Bound ligand 2 1
0T1 5e5h Open in New Window Bound ligand 2 1