Chemical Components in the PDB

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YSC : Summary

Code

YSC

One-letter code

X

Molecule name

[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate

Systematic names

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

Formula

C18 H23 N5 O9 S

Formal charge

0

Molecular weight

485.468 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 N[CH](Cc1ccc(O)cc1)C(=O)N[S](=O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=NC3=O)N
SMILES OpenEye OEToolkits 2.0.6 c1cc(ccc1CC(C(=O)NS(=O)(=O)OCC2C(C(C(O2)N3C=CC(=NC3=O)N)O)O)N)O
Canonical SMILES CACTVS 3.385 N[C@@H](Cc1ccc(O)cc1)C(=O)N[S](=O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=NC3=O)N
Canonical SMILES OpenEye OEToolkits 2.0.6 c1cc(ccc1C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=NC3=O)N)O)O)N)O

IUPAC InChI

InChI=1S/C18H23N5O9S/c19-11(7-9-1-3-10(24)4-2-9)16(27)22-33(29,30)31-8-12-14(25)15(26)17(32-12)23-6-5-13(20)21-18(23)28/h1-6,11-12,14-15,17,24-26H,7-8,19H2,(H,22,27)(H2,20,21,28)/t11-,12+,14+,15+,17+/m0/s1

IUPAC InChI key

CKVJPUGSXWTYBR-LMWHNAIISA-N
YSC

wwPDB Information

Atom count

56 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-08-13

Last modified at

2019-04-12

Status

Released

Obsoleted

Not Assigned



YSC : Atoms of Molecule

Total Number of Atoms: 56
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 2.622 0.847 1.327
2 CA C C1 S N N 0 2.756 -0.317 0.441
3 CB C C2 N N N 0 4.174 -0.881 0.549
4 CG C C3 N Y N 0 5.159 0.132 0.027
5 CD2 C C4 N Y N 0 5.504 0.133 -1.312
6 CE2 C C5 N Y N 0 6.406 1.061 -1.794
7 CZ C C6 N Y N 0 6.967 1.994 -0.932
8 OH O O1 N N N 0 7.855 2.908 -1.404
9 CE1 C C7 N Y N 0 6.619 1.991 0.41
10 CD1 C C8 N Y N 0 5.712 1.064 0.886
11 C C C9 N N N 0 1.762 -1.375 0.848
12 O O O2 N N N 0 1.28 -1.358 1.961
13 NAT N N2 N N N 0 1.409 -2.339 -0.025
14 SBI S S1 N N N 0 0.317 -3.501 0.422
15 OAD O O3 N N N 0 0.133 -4.337 -0.713
16 OAE O O4 N N N 0 0.746 -3.99 1.686
17 O5' O O5 N N N 0 -1.013 -2.801 0.66
18 C5' C C10 N N N 0 -1.689 -2.413 -0.537
19 C4' C C11 R N N 0 -3.006 -1.723 -0.179
20 O4' O O6 N N N 0 -2.752 -0.436 0.426
21 C1' C C12 R N N 0 -3.978 0.31 0.264
22 C2' C C13 R N N 0 -4.467 -0.038 -1.16
23 O2' O O7 N N N 0 -5.891 -0.144 -1.188
24 C3' C C14 S N N 0 -3.813 -1.406 -1.458
25 O3' O O8 N N N 0 -4.813 -2.401 -1.679
26 N1 N N3 N N N 0 -3.72 1.747 0.378
27 C6 C C15 N N N 0 -4.435 2.496 1.264
28 C5 C C16 N N N 0 -4.187 3.824 1.36
29 C4 C C17 N N N 0 -3.194 4.394 0.538
30 N4 N N4 N N N 0 -2.921 5.741 0.616
31 N3 N N5 N N N 0 -2.523 3.626 -0.31
32 C2 C C18 N N N 0 -2.774 2.32 -0.389
33 O2 O O9 N N N 0 -2.144 1.635 -1.177
34 H1 H H1 N N N 0 2.797 0.591 2.288
35 H2 H H2 N N N 0 3.233 1.595 1.036
36 H4 H H4 N N N 0 2.563 -0.014 -0.588
37 H5 H H5 N N N 0 4.398 -1.102 1.593
38 H6 H H6 N N N 0 4.247 -1.796 -0.039
39 H7 H H7 N N N 0 5.067 -0.593 -1.982
40 H8 H H8 N N N 0 6.676 1.061 -2.839
41 H9 H H9 N N N 0 7.448 3.73 -1.711
42 H10 H H10 N N N 0 7.054 2.716 1.083
43 H11 H H11 N N N 0 5.437 1.064 1.931
44 H12 H H12 N N N 0 1.794 -2.352 -0.915
45 H13 H H13 N N N 0 -1.06 -1.724 -1.102
46 H14 H H14 N N N 0 -1.894 -3.296 -1.142
47 H15 H H15 N N N 0 -3.592 -2.35 0.493
48 H16 H H16 N N N 0 -4.713 -0.003 1.006
49 H17 H H17 N N N 0 -4.126 0.712 -1.874
50 H18 H H18 N N N 0 -6.252 -0.361 -2.059
51 H19 H H19 N N N 0 -3.149 -1.332 -2.319
52 H20 H H20 N N N 0 -5.35 -2.252 -2.469
53 H21 H H21 N N N 0 -5.191 2.036 1.883
54 H22 H H22 N N N 0 -4.742 4.436 2.056
55 H23 H H23 N N N 0 -3.413 6.3 1.237
56 H24 H H24 N N N 0 -2.237 6.13 0.049



YSC : Chemical Bonds

Total Number of Bonds: 58
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2 C2 O C doub 1.22 N N
2 C2 N3 C N sing 1.33 N N
3 C2 N1 C N sing 1.35 N N
4 N3 C4 N C doub 1.33 N N
5 O4' C1' O C sing 1.44 N N
6 O4' C4' O C sing 1.44 N N
7 C1' N1 C N sing 1.46 N N
8 C1' C2' C C sing 1.55 N N
9 N1 C6 N C sing 1.36 N N
10 O3' C3' O C sing 1.43 N N
11 C4 N4 C N sing 1.38 N N
12 C4 C5 C C sing 1.41 N N
13 C4' C3' C C sing 1.55 N N
14 C4' C5' C C sing 1.53 N N
15 O2' C2' O C sing 1.43 N N
16 C3' C2' C C sing 1.55 N N
17 C6 C5 C C doub 1.35 N N
18 C5' O5' C O sing 1.43 N N
19 O5' SBI O S sing 1.52 N N
20 CE2 CD2 C C doub 1.38 N Y
21 CE2 CZ C C sing 1.39 N Y
22 CD2 CG C C sing 1.38 N Y
23 SBI OAE S O doub 1.42 N N
24 SBI NAT S N sing 1.66 N N
25 SBI OAD S O doub 1.42 N N
26 NAT C N C sing 1.35 N N
27 OH CZ O C sing 1.36 N N
28 CZ CE1 C C doub 1.39 N Y
29 CB CG C C sing 1.51 N N
30 CB CA C C sing 1.53 N N
31 CG CD1 C C doub 1.38 N Y
32 CA C C C sing 1.51 N N
33 CA N C N sing 1.47 N N
34 C O C O doub 1.21 N N
35 CE1 CD1 C C sing 1.38 N Y
36 N H1 N H sing 1.01 N N
37 N H2 N H sing 1.01 N N
38 CA H4 C H sing 1.09 N N
39 CB H5 C H sing 1.09 N N
40 CB H6 C H sing 1.09 N N
41 CD2 H7 C H sing 1.08 N N
42 CE2 H8 C H sing 1.08 N N
43 OH H9 O H sing 0.97 N N
44 CE1 H10 C H sing 1.08 N N
45 CD1 H11 C H sing 1.08 N N
46 NAT H12 N H sing 0.97 N N
47 C5' H13 C H sing 1.09 N N
48 C5' H14 C H sing 1.09 N N
49 C4' H15 C H sing 1.09 N N
50 C1' H16 C H sing 1.09 N N
51 C2' H17 C H sing 1.09 N N
52 O2' H18 O H sing 0.97 N N
53 C3' H19 C H sing 1.09 N N
54 O3' H20 O H sing 0.97 N N
55 C6 H21 C H sing 1.08 N N
56 C5 H22 C H sing 1.08 N N
57 N4 H23 N H sing 0.97 N N
58 N4 H24 N H sing 0.97 N N



YSC : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
YSC 6hb5 Open in New Window Bound ligand 2 1