Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

QBT : Summary

Code

QBT

One-letter code

X

Molecule name

[(2R,3S,5R)-3-HYDROXY-5-[(5S)-5-METHYL-2,4-DIOXO-1,3-DIAZINAN-1-YL]OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.6.1 [(2R,3S,5R)-3-hydroxy-5-[(5S)-5-methyl-2,4-dioxo-1,3-diazinan-1-yl]oxolan-2-yl]methyl dihydrogen phosphate

Formula

C10 H17 N2 O8 P

Formal charge

0

Molecular weight

324.224 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.352 C[CH]1CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
SMILES OpenEye OEToolkits 1.6.1 CC1CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.352 C[C@H]1CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
Canonical SMILES OpenEye OEToolkits 1.6.1 C[C@H]1CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C10H17N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h5-8,13H,2-4H2,1H3,(H,11,14,15)(H2,16,17,18)/t5-,6-,7+,8+/m0/s1

IUPAC InChI key

PGRQANKWVMVANW-RULNZFCNSA-N
QBT

wwPDB Information

Atom count

38 (21 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-12-08

Last modified at

2022-06-13

Status

Released

Obsoleted

Not Assigned



QBT : Atoms of Molecule

Total Number of Atoms: 38
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P N N N 0 -4.136 1.144 -0.03
2 O1P O O1P N N N 0 -5.413 0.188 0.191
3 O2P O O2P N N N 0 -3.797 1.817 1.244
4 O5' O O5' N N N 0 -2.882 0.26 -0.52
5 C5' C C5' N N N 0 -2.268 -0.739 0.297
6 C4' C C4' R N N 0 -1.112 -1.385 -0.47
7 O4' O O4' N N N 0 -0.053 -0.429 -0.692
8 C3' C C3' S N N 0 -0.435 -2.484 0.387
9 O3' O O3' N N N 0 -1.105 -3.736 0.234
10 C2' C C2' N N N 0 0.987 -2.54 -0.223
11 C1' C C1' R N N 0 1.147 -1.182 -0.934
12 N1 N N1 N N N 0 2.303 -0.467 -0.387
13 C2 C C2 N N N 0 2.293 -0.079 0.899
14 O2 O O2 N N N 0 1.37 -0.418 1.614
15 C5M C C5M N N N 0 5.421 1.328 -1.534
16 N3 N N3 N N N 0 3.278 0.676 1.414
17 C4 C C4 N N N 0 4.184 1.27 0.616
18 O4 O O4 N N N 0 5.112 1.88 1.102
19 C5 C C5 S N N 0 4.045 1.177 -0.882
20 C6 C C6 N N N 0 3.455 -0.191 -1.247
21 O3P O O3P N N Y 0 -4.481 2.251 -1.146
22 H1P H H1P N N N 0 -5.691 -0.286 -0.604
23 H3' H H3' N N N 0 -0.397 -2.19 1.436
24 H5'1 H H5'1 N N N 0 -1.887 -0.28 1.209
25 H5'2 H H5'2 N N N 0 -3.004 -1.501 0.554
26 H4' H H4' N N N 0 -1.464 -1.795 -1.417
27 H1' H H1' N N N 0 1.278 -1.338 -2.005
28 HA H HA N N N 0 -0.718 -4.456 0.751
29 H2'1 H H2'1 N N N 0 1.735 -2.651 0.562
30 H2'2 H H2'2 N N N 0 1.062 -3.358 -0.941
31 H61C H H61C N N N 0 4.208 -0.965 -1.104
32 H62C H H62C N N N 0 3.135 -0.182 -2.289
33 H3 H H3 N N N 0 3.336 0.794 2.375
34 H52 H H52 N N N 0 6.079 0.534 -1.181
35 H53 H H53 N N N 0 5.319 1.26 -2.617
36 H54 H H54 N N N 0 5.845 2.296 -1.269
37 H3P H H3P N N N 0 -5.228 2.821 -0.918
38 H5M H H5M N N N 0 3.385 1.969 -1.237



QBT : Chemical Bonds

Total Number of Bonds: 39
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P O1P P O sing 1.61 N N
2 P O2P P O doub 1.48 N N
3 P O5' P O sing 1.61 N N
4 P O3P P O sing 1.61 N N
5 O5' C5' O C sing 1.43 N N
6 C5' C4' C C sing 1.53 N N
7 C4' O4' C O sing 1.44 N N
8 C4' C3' C C sing 1.55 N N
9 O4' C1' O C sing 1.44 N N
10 C3' O3' C O sing 1.43 N N
11 C3' C2' C C sing 1.55 N N
12 C2' C1' C C sing 1.54 N N
13 C1' N1 C N sing 1.47 N N
14 N1 C2 N C sing 1.34 N N
15 N1 C6 N C sing 1.46 N N
16 C2 O2 C O doub 1.22 N N
17 C2 N3 C N sing 1.34 N N
18 N3 C4 N C sing 1.35 N N
19 C4 O4 C O doub 1.21 N N
20 C4 C5 C C sing 1.51 N N
21 C5 C5M C C sing 1.53 N N
22 O1P H1P O H sing 0.97 N N
23 C5' H5'1 C H sing 1.09 N N
24 C5' H5'2 C H sing 1.09 N N
25 C4' H4' C H sing 1.09 N N
26 C3' H3' C H sing 1.09 N N
27 C1' H1' C H sing 1.09 N N
28 O3' HA O H sing 0.97 N N
29 C2' H2'1 C H sing 1.09 N N
30 C2' H2'2 C H sing 1.09 N N
31 C6 H61C C H sing 1.09 N N
32 C6 H62C C H sing 1.09 N N
33 N3 H3 N H sing 0.97 N N
34 C5 C6 C C sing 1.53 N N
35 C5 H5M C H sing 1.09 N N
36 C5M H52 C H sing 1.09 N N
37 C5M H53 C H sing 1.09 N N
38 C5M H54 C H sing 1.09 N N
39 O3P H3P O H sing 0.97 N N



QBT : Used in PDB Entries

Total Number of PDB Entries: 7
Ligand Code PDB Entry ID Type Total Distinct
QBT 2y1j Open in New Window Polymer component 1 1
QBT 4m94 Open in New Window Polymer component 1 1
QBT 5fuw Open in New Window Bound ligand 1 1
QBT 5fux Open in New Window Bound ligand 2 1
QBT 5fuy Open in New Window Bound ligand 6 1
QBT 6lwh Open in New Window Polymer component 3 1
QBT 6lwi Open in New Window Polymer component 3 1