Chemical Components in the PDB

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QRZ : Summary

Code

QRZ

One-letter code

X

Molecule name

[(2~{R},3~{S},4~{R},5~{R})-5-[6-carbamothioyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 [(2~{R},3~{S},4~{R},5~{R})-5-[6-carbamothioyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate

Formula

C10 H14 N3 O9 P S

Formal charge

0

Molecular weight

383.272 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 NC(=S)C1=CC(=O)NC(=O)N1[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
SMILES OpenEye OEToolkits 2.0.7 C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)C(=S)N
Canonical SMILES CACTVS 3.385 NC(=S)C1=CC(=O)NC(=O)N1[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
Canonical SMILES OpenEye OEToolkits 2.0.7 C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)C(=S)N

IUPAC InChI

InChI=1S/C10H14N3O9PS/c11-8(24)3-1-5(14)12-10(17)13(3)9-7(16)6(15)4(22-9)2-21-23(18,19)20/h1,4,6-7,9,15-16H,2H2,(H2,11,24)(H,12,14,17)(H2,18,19,20)/t4-,6-,7-,9-/m1/s1

IUPAC InChI key

FOTDNYQDMJFRSX-FJGDRVTGSA-N
QRZ

wwPDB Information

Atom count

38 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-07-31

Last modified at

2022-02-18

Status

Released

Obsoleted

Not Assigned



QRZ : 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 C2 C C1 N N N 0 1.775 -1.281 -1.202
2 C3 C C2 N N N 0 3.248 0.826 1.482
3 O3P O O1 N N N 0 -4.634 -2.091 -0.347
4 P P P1 N N N 0 -4.724 -0.731 0.509
5 O1P O O2 N N N 0 -5.738 0.164 -0.093
6 O2P O O3 N N N 0 -5.145 -1.077 2.024
7 O5' O O4 N N N 0 -3.29 0.002 0.504
8 C5' C C3 N N N 0 -2.69 0.529 -0.681
9 C4' C C4 R N N 0 -1.338 1.155 -0.332
10 C3' C C5 S N N 0 -0.726 1.842 -1.574
11 O3' O O5 N N N 0 -0.98 3.248 -1.544
12 C2' C C6 R N N 0 0.788 1.559 -1.452
13 O2' O O6 N N N 0 1.518 2.782 -1.345
14 O4' O O7 N N N 0 -0.387 0.129 0.028
15 C1' C C7 R N N 0 0.912 0.735 -0.151
16 N1 N N1 N N N 0 1.941 -0.298 -0.298
17 C6 C C8 N N N 0 3.071 -0.256 0.491
18 C5 C C9 N N N 0 4.022 -1.219 0.349
19 C4 C C10 N N N 0 3.822 -2.245 -0.613
20 O4 O O8 N N N 0 4.657 -3.118 -0.76
21 N3 N N2 N N N 0 2.699 -2.246 -1.357
22 O2 O O9 N N N 0 0.77 -1.3 -1.887
23 S4 S S1 N N N 0 2.573 0.671 3.048
24 N5 N N3 N N N 0 3.941 1.934 1.154
25 H4 H H4 N N N 0 -3.341 1.289 -1.111
26 H1 H H1 N N N 0 -3.987 -2.726 -0.01
27 H2 H H2 N N N 0 -6.0 -1.521 2.103
28 H3 H H3 N N N 0 -2.543 -0.275 -1.402
29 H5 H H5 N N N 0 -1.451 1.872 0.481
30 H6 H H6 N N N 0 -1.125 1.402 -2.488
31 H7 H H7 N N N 0 -0.618 3.729 -2.3
32 H8 H H8 N N N 0 1.138 0.979 -2.306
33 H9 H H9 N N N 0 1.426 3.364 -2.112
34 H10 H H10 N N N 0 1.146 1.387 0.69
35 H11 H H11 N N N 0 4.914 -1.203 0.957
36 H12 H H12 N N N 0 2.558 -2.945 -2.015
37 H13 H H13 N N N 0 4.324 2.021 0.267
38 H14 H H14 N N N 0 4.057 2.644 1.804



QRZ : 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 S4 C3 S C doub 1.71 N N
2 N5 C3 N C sing 1.35 N N
3 C3 C6 C C sing 1.48 N N
4 C5 C6 C C doub 1.36 N N
5 C5 C4 C C sing 1.42 N N
6 C6 N1 C N sing 1.38 N N
7 O4 C4 O C doub 1.22 N N
8 C4 N3 C N sing 1.35 N N
9 N1 C1' N C sing 1.47 N N
10 N1 C2 N C sing 1.35 N N
11 C1' O4' C O sing 1.44 N N
12 C1' C2' C C sing 1.54 N N
13 O4' C4' O C sing 1.44 N N
14 N3 C2 N C sing 1.35 N N
15 O2' C2' O C sing 1.43 N N
16 C2 O2 C O doub 1.22 N N
17 O3' C3' O C sing 1.43 N N
18 C2' C3' C C sing 1.55 N N
19 C4' C3' C C sing 1.55 N N
20 C4' C5' C C sing 1.53 N N
21 C5' O5' C O sing 1.43 N N
22 O5' P O P sing 1.61 N N
23 O1P P O P doub 1.48 N N
24 P O3P P O sing 1.61 N N
25 P O2P P O sing 1.61 N N
26 O3P H1 O H sing 0.97 N N
27 O2P H2 O H sing 0.97 N N
28 C5' H3 C H sing 1.09 N N
29 C5' H4 C H sing 1.09 N N
30 C4' H5 C H sing 1.09 N N
31 C3' H6 C H sing 1.09 N N
32 O3' H7 O H sing 0.97 N N
33 C2' H8 C H sing 1.09 N N
34 O2' H9 O H sing 0.97 N N
35 C1' H10 C H sing 1.09 N N
36 C5 H11 C H sing 1.08 N N
37 N3 H12 N H sing 0.97 N N
38 N5 H13 N H sing 0.97 N N
39 N5 H14 N H sing 0.97 N N



QRZ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
QRZ 6zx3 Open in New Window Bound ligand 1 1