Chemical Components in the PDB

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0L7 : Summary

Code

0L7

One-letter code

X

Molecule name

2-amino-5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one

Systematic names

ProgramVersionName
ACDLabs 12.01 2-amino-5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
OpenEye OEToolkits 1.7.6 [[(2R,3S,5R)-5-[2-azanyl-5-(5-azanylpent-1-ynyl)-4-oxidanylidene-3H-pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

Formula

C16 H24 N5 O13 P3

Formal charge

0

Molecular weight

587.309 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2c1N=C(N)NC(=O)c1c(C#CCCCN)c2)CC3O
SMILES CACTVS 3.370 NCCCC#Cc1cn([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)c3N=C(N)NC(=O)c13
SMILES OpenEye OEToolkits 1.7.6 c1c(c2c(n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N)C#CCCCN
Canonical SMILES CACTVS 3.370 NCCCC#Cc1cn([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)c3N=C(N)NC(=O)c13
Canonical SMILES OpenEye OEToolkits 1.7.6 c1c(c2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N)C#CCCCN

IUPAC InChI

InChI=1S/C16H24N5O13P3/c17-5-3-1-2-4-9-7-21(14-13(9)15(23)20-16(18)19-14)12-6-10(22)11(32-12)8-31-36(27,28)34-37(29,30)33-35(24,25)26/h7,10-12,22H,1,3,5-6,8,17H2,(H,27,28)(H,29,30)(H2,24,25,26)(H3,18,19,20,23)/t10-,11+,12+/m0/s1

IUPAC InChI key

XIWGGMXHUSVMFH-QJPTWQEYSA-N
0L7

wwPDB Information

Atom count

61 (37 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-02-08

Last modified at

2012-05-11

Status

Released

Obsoleted

Not Assigned



0L7 : Atoms of Molecule

Total Number of Atoms: 61
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O6 O O6 N N N 0 7.187 0.595 -1.813
2 C6 C C6 N N N 0 6.556 -0.436 -1.656
3 N1 N N1 N N N 0 7.023 -1.614 -2.127
4 C2 C C2 N N N 0 6.305 -2.758 -1.943
5 N2 N N2 N N N 0 6.802 -3.941 -2.43
6 N3 N N3 N N N 0 5.152 -2.765 -1.314
7 C5 C C5 N Y N 0 5.321 -0.431 -0.975
8 C4 C C4 N Y N 0 4.623 -1.635 -0.82
9 C7 C C7 N Y N 0 4.501 0.606 -0.335
10 C32 C C32 N N N 0 4.799 2.004 -0.248
11 C33 C C33 N N N 0 5.043 3.15 -0.176
12 C34 C C34 N N N 0 5.35 4.587 -0.087
13 C35 C C35 N N N 0 4.225 5.303 0.663
14 C36 C C36 N N N 0 4.544 6.797 0.756
15 N37 N N37 N N N 0 3.464 7.484 1.476
16 C8 C C8 N Y N 0 3.402 -0.024 0.157
17 N9 N N9 N Y N 0 3.471 -1.358 -0.14
18 C1' C C1* R N N 0 2.461 -2.351 0.232
19 C2' C C2* N N N 0 2.859 -3.033 1.556
20 C3' C C3* S N N 0 1.671 -2.744 2.504
21 O3' O O3* N N N 0 1.355 -3.894 3.292
22 O4' O O4* N N N 0 1.195 -1.704 0.445
23 C4' C C4* R N N 0 0.528 -2.426 1.506
24 C5' C C5* N N N 0 -0.537 -1.55 2.167
25 O5' O O5* N N N 0 -1.632 -1.369 1.266
26 PA P PA N N N 0 -2.935 -0.498 1.634
27 O1A O O1A N N N 0 -3.728 -1.204 2.844
28 O2A O O2A N N N 0 -2.52 0.863 2.042
29 O3A O O3A N N N 0 -3.897 -0.402 0.346
30 PB P PB N N N 0 -5.082 0.595 -0.093
31 O1B O O1B N N N 0 -5.915 0.92 1.086
32 O2B O O2B N N N 0 -4.45 1.949 -0.693
33 O3B O O3B N N N 0 -5.993 -0.115 -1.214
34 PG P PG N N N 0 -7.451 0.188 -1.827
35 O3G O O3G N N N 0 -8.364 0.611 -0.741
36 O2G O O2G N N N 0 -7.34 1.361 -2.923
37 O1G O O1G N N N 0 -8.028 -1.145 -2.523
38 H1 H H1 N N N 0 7.872 -1.646 -2.596
39 H2 H H2 N N N 0 7.653 -3.953 -2.897
40 H3 H H3 N N N 0 6.304 -4.764 -2.308
41 H4 H H4 N N N 0 6.289 4.726 0.449
42 H5 H H5 N N N 0 5.44 5.003 -1.091
43 H6 H H6 N N N 0 3.286 5.165 0.127
44 H7 H H7 N N N 0 4.136 4.887 1.667
45 H8 H H8 N N N 0 5.483 6.935 1.292
46 H9 H H9 N N N 0 4.633 7.212 -0.248
47 H10 H H10 N N N 0 3.318 7.074 2.386
48 H14 H H14 N N N 0 2.367 -3.098 -0.556
49 H11 H H11 N N N 0 3.651 8.472 1.551
50 H13 H H13 N N N 0 2.594 0.455 0.689
51 H15 H H15 N N N 0 2.98 -4.106 1.411
52 H16 H H16 N N N 0 3.778 -2.596 1.948
53 H17 H H17 N N N 0 1.881 -1.885 3.141
54 H18 H H18 N N N 0 2.075 -4.186 3.868
55 H19 H H19 N N N 0 0.087 -3.346 1.122
56 H20 H H20 N N N 0 -0.892 -2.034 3.077
57 H21 H H21 N N N 0 -0.107 -0.58 2.416
58 H24 H H24 N N N 0 -6.757 1.152 -3.665
59 H22 H H22 N N N 0 -4.03 -2.101 2.646
60 H23 H H23 N N N 0 -3.891 1.811 -1.47
61 H25 H H25 N N N 0 -8.905 -1.036 -2.914



0L7 : Chemical Bonds

Total Number of Bonds: 63
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3G PG O P doub 1.48 N N
2 O1G PG O P sing 1.61 N N
3 PG O2G P O sing 1.61 N N
4 PG O3B P O sing 1.61 N N
5 O1B PB O P doub 1.48 N N
6 O2A PA O P doub 1.48 N N
7 O3B PB O P sing 1.61 N N
8 PB O2B P O sing 1.61 N N
9 PB O3A P O sing 1.61 N N
10 C5' O5' C O sing 1.43 N N
11 C5' C4' C C sing 1.53 N N
12 PA O3A P O sing 1.61 N N
13 PA O5' P O sing 1.61 N N
14 PA O1A P O sing 1.61 N N
15 O3' C3' O C sing 1.43 N N
16 C4' C3' C C sing 1.55 N N
17 C4' O4' C O sing 1.45 N N
18 C3' C2' C C sing 1.55 N N
19 O4' C1' O C sing 1.44 N N
20 C2' C1' C C sing 1.54 N N
21 C1' N9 C N sing 1.46 N N
22 C8 N9 C N sing 1.37 N Y
23 C8 C7 C C doub 1.36 N Y
24 N9 C4 N C sing 1.37 N Y
25 C7 C32 C C sing 1.43 N N
26 C7 C5 C C sing 1.47 N Y
27 C32 C33 C C trip 1.17 N N
28 C4 N3 C N sing 1.34 N N
29 C4 C5 C C doub 1.4 N Y
30 C33 C34 C C sing 1.47 N N
31 C34 C35 C C sing 1.53 N N
32 N3 C2 N C doub 1.31 N N
33 C5 C6 C C sing 1.41 N N
34 C35 C36 C C sing 1.53 N N
35 C2 N2 C N sing 1.37 N N
36 C2 N1 C N sing 1.36 N N
37 C6 N1 C N sing 1.35 N N
38 C6 O6 C O doub 1.22 N N
39 C36 N37 C N sing 1.47 N N
40 N1 H1 N H sing 0.97 N N
41 N2 H2 N H sing 0.97 N N
42 N2 H3 N H sing 0.97 N N
43 C34 H4 C H sing 1.09 N N
44 C34 H5 C H sing 1.09 N N
45 C35 H6 C H sing 1.09 N N
46 C35 H7 C H sing 1.09 N N
47 C36 H8 C H sing 1.09 N N
48 C36 H9 C H sing 1.09 N N
49 N37 H10 N H sing 1.01 N N
50 N37 H11 N H sing 1.01 N N
51 C8 H13 C H sing 1.08 N N
52 C1' H14 C H sing 1.09 N N
53 C2' H15 C H sing 1.09 N N
54 C2' H16 C H sing 1.09 N N
55 C3' H17 C H sing 1.09 N N
56 O3' H18 O H sing 0.97 N N
57 C4' H19 C H sing 1.09 N N
58 C5' H20 C H sing 1.09 N N
59 C5' H21 C H sing 1.09 N N
60 O1A H22 O H sing 0.97 N N
61 O2B H23 O H sing 0.97 N N
62 O2G H24 O H sing 0.97 N N
63 O1G H25 O H sing 0.97 N N



0L7 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
0L7 4dfp Open in New Window Bound ligand 1 1