Chemical Components in the PDB

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0R7 : Summary

Code

0R7

One-letter code

X

Molecule name

[[(2S,5R)-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-1-yl]oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.7.6 [[(2S,5R)-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-1-yl]oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

Formula

C19 H20 N3 O12 P3

Formal charge

0

Molecular weight

575.296 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.370 NC1=NC(=O)N(C=C1C#Cc2ccc(cc2)C#C)[CH]3CC[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
SMILES OpenEye OEToolkits 1.7.6 C#Cc1ccc(cc1)C#CC2=CN(C(=O)N=C2N)C3CCC(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O
Canonical SMILES CACTVS 3.370 NC1=NC(=O)N(C=C1C#Cc2ccc(cc2)C#C)[C@H]3CC[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
Canonical SMILES OpenEye OEToolkits 1.7.6 C#Cc1ccc(cc1)C#CC2=CN(C(=O)N=C2N)[C@H]3CC[C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O

IUPAC InChI

InChI=1S/C19H20N3O12P3/c1-2-13-3-5-14(6-4-13)7-8-15-11-22(19(23)21-18(15)20)17-10-9-16(32-17)12-31-36(27,28)34-37(29,30)33-35(24,25)26/h1,3-6,11,16-17H,9-10,12H2,(H,27,28)(H,29,30)(H2,20,21,23)(H2,24,25,26)/t16-,17+/m0/s1

IUPAC InChI key

PROFTMDIPXHDEG-DLBZAZTESA-N
0R7

wwPDB Information

Atom count

57 (37 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-04-27

Last modified at

2013-04-19

Status

Released

Obsoleted

Not Assigned



0R7 : Atoms of Molecule

Total Number of Atoms: 57
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O5' O O5' N N N 0 -1.242 1.78 -1.268
2 P1 P P1 N N N 0 -2.109 0.437 -1.455
3 O1 O O1 N N N 0 -3.36 0.46 -0.443
4 P2 P P2 N N N 0 -4.332 -0.674 0.16
5 O3 O O3 N N N 0 -5.689 0.011 0.692
6 P3 P P3 N N N 0 -7.139 -0.554 1.104
7 O5 O O5 N N N 0 -7.076 -1.157 2.596
8 O6 O O6 N N N 0 -8.215 0.642 1.054
9 O7 O O7 N N N 0 -7.541 -1.619 0.159
10 O8 O O8 N N N 0 -3.594 -1.421 1.38
11 O9 O O9 N N N 0 -4.657 -1.658 -0.897
12 O10 O O10 N N N 0 -2.646 0.352 -2.971
13 O11 O O11 N N N 0 -1.262 -0.742 -1.166
14 C1' C C1' R N N 0 2.164 4.15 -0.023
15 N1 N N1 N N N 0 3.257 3.325 0.499
16 C6 C C6 N N N 0 3.253 1.985 0.266
17 C5 C C5 N N N 0 4.289 1.218 0.763
18 C1 C C1 N N N 0 4.33 -0.196 0.545
19 C3 C C3 N N N 0 4.364 -1.356 0.366
20 N2 N N2 N N N 0 5.265 3.208 1.698
21 C4 C C4 N N N 0 5.346 1.897 1.522
22 C2 C C2 N N N 0 4.248 3.905 1.194
23 O2 O O2 N N N 0 4.214 5.111 1.374
24 N3 N N3 N N N 0 6.401 1.186 2.04
25 O4' O O4' N N N 0 0.984 3.353 -0.176
26 C4' C C4' S N N 0 0.55 3.378 -1.545
27 C3' C C3' N N N 0 1.823 3.704 -2.367
28 C2' C C2' N N N 0 2.542 4.701 -1.415
29 C5' C C5' N N N 0 -0.0080 2.012 -1.95
30 C01 C C01 N Y N 0 4.405 -2.771 0.147
31 C02 C C02 N Y N 0 3.39 -3.396 -0.585
32 C03 C C03 N Y N 0 3.43 -4.745 -0.793
33 C04 C C04 N Y N 0 4.486 -5.501 -0.276
34 C05 C C05 N Y N 0 5.5 -4.878 0.455
35 C C C N Y N 0 5.465 -3.527 0.66
36 C7 C C7 N N N 0 4.527 -6.916 -0.495
37 C8 C C8 N N N 0 4.562 -8.075 -0.675
38 H1 H H1 N N N 0 -6.818 -0.513 3.27
39 H2 H H2 N N N 0 -9.113 0.374 1.291
40 H3 H H3 N N N 0 -3.351 -0.835 2.111
41 H4 H H4 N N N 0 -3.21 1.094 -3.23
42 H5 H H5 N N N 0 1.967 4.976 0.66
43 H6 H H6 N N N 0 2.453 1.529 -0.298
44 H7 H H7 N N N 0 6.451 0.227 1.907
45 H8 H H8 N N N 0 7.095 1.644 2.54
46 H9 H H9 N N N 0 -0.203 4.153 -1.69
47 H10 H H10 N N N 0 2.425 2.81 -2.529
48 H11 H H11 N N N 0 1.567 4.18 -3.314
49 H12 H H12 N N N 0 2.159 5.712 -1.55
50 H13 H H13 N N N 0 3.622 4.67 -1.565
51 H14 H H14 N N N 0 0.707 1.234 -1.682
52 H15 H H15 N N N 0 -0.179 1.993 -3.026
53 H16 H H16 N N N 0 2.574 -2.812 -0.984
54 H17 H H17 N N N 0 2.646 -5.228 -1.358
55 H18 H H18 N N N 0 6.315 -5.463 0.855
56 H19 H H19 N N N 0 6.251 -3.045 1.221
57 H20 H H20 N N N 0 4.592 -9.113 -0.835



0R7 : Chemical Bonds

Total Number of Bonds: 59
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O7 P3 O P doub 1.48 N N
2 O6 P3 O P sing 1.61 N N
3 P3 O5 P O sing 1.61 N N
4 P3 O3 P O sing 1.61 N N
5 O9 P2 O P doub 1.48 N N
6 O11 P1 O P doub 1.48 N N
7 O3 P2 O P sing 1.61 N N
8 P2 O8 P O sing 1.61 N N
9 P2 O1 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 P1 O1 P O sing 1.61 N N
13 P1 O5' P O sing 1.61 N N
14 P1 O10 P O sing 1.61 N N
15 C4' C3' C C sing 1.55 N N
16 C4' O4' C O sing 1.44 N N
17 C3' C2' C C sing 1.55 N N
18 O4' C1' O C sing 1.43 N N
19 C2' C1' C C sing 1.54 N N
20 C1' N1 C N sing 1.47 N N
21 C6 N1 C N sing 1.36 N N
22 C6 C5 C C doub 1.38 N N
23 N1 C2 N C sing 1.34 N N
24 C02 C03 C C doub 1.37 N Y
25 C02 C01 C C sing 1.4 N Y
26 C03 C04 C C sing 1.4 N Y
27 C1 C3 C C trip 1.17 N N
28 C1 C5 C C sing 1.43 N N
29 C3 C01 C C sing 1.43 N N
30 C5 C4 C C sing 1.47 N N
31 C01 C C C doub 1.4 N Y
32 C04 C7 C C sing 1.43 N N
33 C04 C05 C C doub 1.4 N Y
34 C2 O2 C O doub 1.22 N N
35 C2 N2 C N sing 1.33 N N
36 C7 C8 C C trip 1.17 N N
37 C C05 C C sing 1.37 N Y
38 C4 N2 C N doub 1.33 N N
39 C4 N3 C N sing 1.37 N N
40 O5 H1 O H sing 0.97 N N
41 O6 H2 O H sing 0.97 N N
42 O8 H3 O H sing 0.97 N N
43 O10 H4 O H sing 0.97 N N
44 C1' H5 C H sing 1.09 N N
45 C6 H6 C H sing 1.08 N N
46 N3 H7 N H sing 0.97 N N
47 N3 H8 N H sing 0.97 N N
48 C4' H9 C H sing 1.09 N N
49 C3' H10 C H sing 1.09 N N
50 C3' H11 C H sing 1.09 N N
51 C2' H12 C H sing 1.09 N N
52 C2' H13 C H sing 1.09 N N
53 C5' H14 C H sing 1.09 N N
54 C5' H15 C H sing 1.09 N N
55 C02 H16 C H sing 1.08 N N
56 C03 H17 C H sing 1.08 N N
57 C05 H18 C H sing 1.08 N N
58 C H19 C H sing 1.08 N N
59 C8 H20 C H sing 1.05 N N



0R7 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
0R7 4elv Open in New Window Bound ligand 1 1