Chemical Components in the PDB

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0R8 : Summary

Code

0R8

One-letter code

C

Molecule name

[(2S,5R)-5-{4-amino-5-[(4-ethynylphenyl)ethynyl]-2-oxopyrimidin-1(2H)-yl}tetrahydrofuran-2-yl]methyl dihydrogen phosphate

Systematic names

ProgramVersionName
ACDLabs 12.01 [(2S,5R)-5-{4-amino-5-[(4-ethynylphenyl)ethynyl]-2-oxopyrimidin-1(2H)-yl}tetrahydrofuran-2-yl]methyl dihydrogen phosphate
OpenEye OEToolkits 1.7.6 [(2S,5R)-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-1-yl]oxolan-2-yl]methyl dihydrogen phosphate

Formula

C19 H18 N3 O6 P

Formal charge

0

Molecular weight

415.336 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC3OC(N2C(=O)N=C(N)C(C#Cc1ccc(C#C)cc1)=C2)CC3
SMILES CACTVS 3.370 NC1=NC(=O)N(C=C1C#Cc2ccc(cc2)C#C)[CH]3CC[CH](CO[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)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)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)O

IUPAC InChI

InChI=1S/C19H18N3O6P/c1-2-13-3-5-14(6-4-13)7-8-15-11-22(19(23)21-18(15)20)17-10-9-16(28-17)12-27-29(24,25)26/h1,3-6,11,16-17H,9-10,12H2,(H2,20,21,23)(H2,24,25,26)/t16-,17+/m0/s1

IUPAC InChI key

IXTAGUCYLSQFGM-DLBZAZTESA-N
0R8

wwPDB Information

Atom count

47 (29 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DC

Defined at

2012-04-27

Last modified at

2013-04-19

Status

Released

Obsoleted

Not Assigned



0R8 : Atoms of Molecule

Total Number of Atoms: 47
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C N Y N 0 4.875 -1.249 -0.131
2 C01 C C01 N Y N 0 3.688 -0.528 0.043
3 C02 C C02 N Y N 0 3.738 0.844 0.314
4 C03 C C03 N Y N 0 4.944 1.479 0.402
5 C04 C C04 N Y N 0 6.128 0.759 0.221
6 C05 C C05 N Y N 0 6.08 -0.611 -0.05
7 C1 C C1 N N N 0 1.388 -1.742 -0.124
8 C1' C C1' R N N 0 -3.497 -1.672 0.034
9 C2 C C2 N N N 0 -2.258 -3.712 -0.394
10 C2' C C2' N N N 0 -3.938 -1.743 1.512
11 C3 C C3 N N N 0 2.424 -1.195 -0.049
12 C3' C C3' N N N 0 -3.444 -0.376 2.066
13 C4 C C4 N N N 0 0.048 -3.848 -0.493
14 C4' C C4' S N N 0 -3.646 0.534 0.829
15 C5 C C5 N N N 0 0.125 -2.409 -0.217
16 C5' C C5' N N N 0 -2.706 1.739 0.896
17 C6 C C6 N N N 0 -1.059 -1.717 -0.047
18 C7 C C7 N N N 0 7.392 1.426 0.313
19 C8 C C8 N N N 0 8.428 1.973 0.388
20 H1' H H1' N N N 0 -4.266 -2.11 -0.602
21 H14 H H14 N N N 0 2.823 1.4 0.454
22 H15 H H15 N N N 0 4.982 2.538 0.611
23 H16 H H16 N N N 0 6.995 -1.166 -0.19
24 H17 H H17 N N N 0 4.838 -2.309 -0.336
25 H18 H H18 N N N 0 9.355 2.462 0.455
26 H2' H H2' N N N 0 -5.022 -1.825 1.592
27 H2'' H H2'' N N N 0 -3.446 -2.57 2.025
28 H3' H H3' N N N 0 -2.392 -0.424 2.351
29 H3'' H H3'' N N N 0 -4.06 -0.046 2.902
30 H41 H H41 N N N 0 2.06 -4.159 -0.614
31 H42 H H42 N N N 0 1.131 -5.538 -0.854
32 H5' H H5' N N N 0 -1.673 1.398 0.828
33 H5'' H H5'' N N N 0 -2.854 2.263 1.84
34 H6 H H6 N N N 0 -1.051 -0.656 0.157
35 H7 H H7 N N N 0 -4.683 0.865 0.769
36 HOP2 H HOP2 N N N 0 -0.528 3.129 -1.566
37 HOP3 H H1 N N Y 0 -2.417 5.641 -1.86
38 N1 N N1 N N N 0 -2.235 -2.393 -0.144
39 N3 N N3 N N N 0 -1.145 -4.421 -0.569
40 N4 N N4 N N N 0 1.192 -4.588 -0.671
41 O2 O O2 N N N 0 -3.335 -4.279 -0.467
42 O4' O O4' N N N 0 -3.319 -0.291 -0.301
43 O5' O O5' N N N 0 -2.987 2.624 -0.19
44 OP1 O OP1 N N N 0 -2.251 4.83 0.793
45 OP2 O OP2 N N N 0 -0.647 3.671 -0.774
46 OP3 O OP3 N N Y 0 -2.851 4.8 -1.658
47 P P P N N N 0 -2.186 4.0 -0.43



0R8 : Chemical Bonds

Total Number of Bonds: 49
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OP2 P O P sing 1.61 N N
2 C5' C4' C C sing 1.53 N N
3 C5' O5' C O sing 1.43 N N
4 C4' C3' C C sing 1.55 N N
5 C4' O4' C O sing 1.44 N N
6 C3' C2' C C sing 1.56 N N
7 C2' C1' C C sing 1.54 N N
8 O5' P O P sing 1.61 N N
9 P OP1 P O doub 1.48 N N
10 O4' C1' O C sing 1.43 N N
11 C1' N1 C N sing 1.46 N N
12 N1 C6 N C sing 1.36 N N
13 N1 C2 N C sing 1.34 N N
14 O2 C2 O C doub 1.22 N N
15 C6 C5 C C doub 1.38 N N
16 C2 N3 C N sing 1.33 N N
17 C5 C1 C C sing 1.43 N N
18 C5 C4 C C sing 1.47 N N
19 N3 C4 N C doub 1.33 N N
20 C1 C3 C C trip 1.17 N N
21 C4 N4 C N sing 1.37 N N
22 C3 C01 C C sing 1.43 N N
23 C02 C01 C C doub 1.4 N Y
24 C02 C03 C C sing 1.37 N Y
25 C01 C C C sing 1.4 N Y
26 C03 C04 C C doub 1.4 N Y
27 C C05 C C doub 1.37 N Y
28 C04 C05 C C sing 1.4 N Y
29 C04 C7 C C sing 1.43 N N
30 C7 C8 C C trip 1.17 N N
31 OP2 HOP2 O H sing 0.97 N N
32 C1' H1' C H sing 1.09 N N
33 C6 H6 C H sing 1.08 N N
34 N4 H41 N H sing 0.97 N N
35 N4 H42 N H sing 0.97 N N
36 C4' H7 C H sing 1.09 N N
37 C3' H3' C H sing 1.09 N N
38 C3' H3'' C H sing 1.09 N N
39 C2' H2' C H sing 1.09 N N
40 C2' H2'' C H sing 1.09 N N
41 C5' H5' C H sing 1.09 N N
42 C5' H5'' C H sing 1.09 N N
43 C02 H14 C H sing 1.08 N N
44 C03 H15 C H sing 1.08 N N
45 C05 H16 C H sing 1.08 N N
46 C H17 C H sing 1.08 N N
47 C8 H18 C H sing 1.05 N N
48 P OP3 P O sing 1.61 N N
49 OP3 HOP3 O H sing 0.97 N N



0R8 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
0R8 4elv Open in New Window Polymer component 1 1