Chemical Components in the PDB

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BQL : Summary

Code

BQL

One-letter code

X

Molecule name

[(2~{S})-2-azanyl-3-oxidanylidene-propyl] [(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 [(2~{S})-2-azanyl-3-oxidanylidene-propyl] [(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate

Formula

C12 H18 N3 O10 P

Formal charge

0

Molecular weight

395.259 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 N[CH](CO[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O)C=O
SMILES OpenEye OEToolkits 2.0.6 C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OCC(C=O)N)O)O
Canonical SMILES CACTVS 3.385 N[C@@H](CO[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O)C=O
Canonical SMILES OpenEye OEToolkits 2.0.6 C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OC[C@@H](C=O)N)O)O

IUPAC InChI

InChI=1S/C12H18N3O10P/c13-6(3-16)4-23-26(21,22)24-5-7-9(18)10(19)11(25-7)15-2-1-8(17)14-12(15)20/h1-3,6-7,9-11,18-19H,4-5,13H2,(H,21,22)(H,14,17,20)/t6-,7-,9-,10-,11-/m1/s1

IUPAC InChI key

DGKQNNIXYUXPCL-JBSYKWBFSA-N
BQL

wwPDB Information

Atom count

44 (26 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-03-04

Last modified at

2019-03-15

Status

Released

Obsoleted

Not Assigned



BQL : Atoms of Molecule

Total Number of Atoms: 44
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N1 N N N 0 -5.219 2.275 -1.112
2 CA C C1 S N N 0 -5.83 0.947 -0.973
3 C C C2 N N N 0 -7.291 1.099 -0.635
4 O O O1 N N N 0 -7.773 2.201 -0.522
5 CB C C3 N N N 0 -5.126 0.176 0.146
6 C1' C C4 R N N 0 2.866 -0.627 -0.877
7 C2 C C5 N N N 0 3.318 1.185 0.679
8 C2' C C6 R N N 0 3.268 -1.787 0.07
9 C3 C C7 R N N 0 0.908 -1.817 -0.54
10 C3' C C8 S N N 0 2.043 -2.728 -0.032
11 C4 C C9 N N N 0 4.84 2.895 0.212
12 C5 C C10 N N N 0 5.116 2.293 -1.039
13 C5' C C11 N N N 0 -0.251 -1.824 0.459
14 C6 C C12 N N N 0 4.469 1.156 -1.378
15 N1 N N2 N N N 0 3.567 0.605 -0.51
16 N3 N N3 N N N 0 3.944 2.32 1.04
17 O1 O O2 N N N 0 2.296 -3.78 -0.965
18 O2 O O3 N N N 0 2.513 0.678 1.436
19 O3 O O4 N N N 0 4.451 -2.438 -0.396
20 O4 O O5 N N N 0 5.407 3.922 0.537
21 OP2 O O9 N N N 0 -3.294 -2.18 1.074
22 O4' O O6 N N N 0 1.446 -0.489 -0.656
23 O5' O O7 N N N 0 -1.34 -1.066 -0.071
24 OP1 O O8 N N N 0 -2.466 -0.008 2.056
25 OP3 O O10 N N N 0 -3.768 -0.07 -0.227
26 P P P1 N N N 0 -2.73 -0.86 0.716
27 H1 H H1 N N N 0 -5.623 2.78 -1.887
28 H2 H H2 N N N 0 -5.299 2.802 -0.255
29 H4 H H4 N N N 0 -5.729 0.4 -1.91
30 H5 H H5 N N N 0 -7.907 0.223 -0.494
31 H6 H H6 N N N 0 -5.15 0.764 1.063
32 H7 H H7 N N N 0 -5.635 -0.773 0.31
33 H8 H H8 N N N 0 3.069 -0.891 -1.915
34 H9 H H9 N N N 0 3.399 -1.428 1.091
35 H10 H H10 N N N 0 0.561 -2.166 -1.513
36 H11 H H11 N N N 0 1.794 -3.137 0.947
37 H12 H H12 N N N 0 5.83 2.738 -1.716
38 H13 H H13 N N N 0 -0.574 -2.85 0.635
39 H14 H H14 N N N 0 0.077 -1.38 1.399
40 H15 H H15 N N N 0 4.667 0.683 -2.328
41 H16 H H16 N N N 0 3.749 2.728 1.898
42 H17 H H17 N N N 0 3.039 -4.349 -0.724
43 H18 H H18 N N N 0 4.743 -3.171 0.164
44 H19 H H19 N N N 0 -2.095 0.871 1.897



BQL : Chemical Bonds

Total Number of Bonds: 45
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C5 C6 C C doub 1.35 N N
2 C5 C4 C C sing 1.42 N N
3 C6 N1 C N sing 1.37 N N
4 O4 C4 O C doub 1.22 N N
5 C4 N3 C N sing 1.35 N N
6 N1 C1' N C sing 1.46 N N
7 N1 C2 N C sing 1.35 N N
8 O3 C2' O C sing 1.43 N N
9 C1' C2' C C sing 1.55 N N
10 C1' O4' C O sing 1.44 N N
11 N3 C2 N C sing 1.35 N N
12 C2' C3' C C sing 1.55 N N
13 C2 O2 C O doub 1.22 N N
14 O4' C3 O C sing 1.44 N N
15 O1 C3' O C sing 1.43 N N
16 C3' C3 C C sing 1.54 N N
17 C3 C5' C C sing 1.53 N N
18 N CA N C sing 1.47 N N
19 O C O C doub 1.21 N N
20 O5' C5' O C sing 1.43 N N
21 O5' P O P sing 1.61 N N
22 CA C C C sing 1.51 N N
23 CA CB C C sing 1.53 N N
24 OP2 P O P doub 1.48 N N
25 P OP3 P O sing 1.61 N N
26 P OP1 P O sing 1.61 N N
27 OP3 CB O C sing 1.43 N N
28 N H1 N H sing 1.01 N N
29 N H2 N H sing 1.01 N N
30 CA H4 C H sing 1.09 N N
31 C H5 C H sing 1.08 N N
32 CB H6 C H sing 1.09 N N
33 CB H7 C H sing 1.09 N N
34 C1' H8 C H sing 1.09 N N
35 C2' H9 C H sing 1.09 N N
36 C3 H10 C H sing 1.09 N N
37 C3' H11 C H sing 1.09 N N
38 C5 H12 C H sing 1.08 N N
39 C5' H13 C H sing 1.09 N N
40 C5' H14 C H sing 1.09 N N
41 C6 H15 C H sing 1.08 N N
42 N3 H16 N H sing 0.97 N N
43 O1 H17 O H sing 0.97 N N
44 O3 H18 O H sing 0.97 N N
45 OP1 H19 O H sing 0.97 N N



BQL : Used in PDB Entries

Total Number of PDB Entries: 0
Ligand Code PDB Entry ID Type Total Distinct