Chemical Components in the PDB

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KVE : Summary

Code

KVE

One-letter code

X

Molecule name

(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-(4-naphthalen-2-yl-1,3-thiazol-2-yl)oxane-3,4,5-triol

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-(4-naphthalen-2-yl-1,3-thiazol-2-yl)oxane-3,4,5-triol

Formula

C19 H19 N O5 S

Formal charge

0

Molecular weight

373.423 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)c2scc(n2)c3ccc4ccccc4c3
SMILES OpenEye OEToolkits 2.0.7 c1ccc2cc(ccc2c1)c3csc(n3)C4C(C(C(C(O4)CO)O)O)O
Canonical SMILES CACTVS 3.385 OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)c2scc(n2)c3ccc4ccccc4c3
Canonical SMILES OpenEye OEToolkits 2.0.7 c1ccc2cc(ccc2c1)c3csc(n3)[C@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O

IUPAC InChI

InChI=1S/C19H19NO5S/c21-8-14-15(22)16(23)17(24)18(25-14)19-20-13(9-26-19)12-6-5-10-3-1-2-4-11(10)7-12/h1-7,9,14-18,21-24H,8H2/t14-,15-,16+,17-,18-/m1/s1

IUPAC InChI key

NRPWZWOXDUROHO-UYTYNIKBSA-N
KVE

wwPDB Information

Atom count

45 (26 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-06-29

Last modified at

2020-02-14

Status

Released

Obsoleted

Not Assigned



KVE : Atoms of Molecule

Total Number of Atoms: 45
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 0.875 -0.221 0.312
2 C3 C C2 N Y N 0 -1.081 -1.012 1.584
3 C4 C C3 N Y N 0 -1.347 -0.345 0.442
4 C6 C C4 N Y N 0 -2.726 -0.088 -0.04
5 C10 C C5 N Y N 0 -4.177 0.766 -1.755
6 C14 C C6 N Y N 0 -7.665 0.297 -0.667
7 C7 C C7 N Y N 0 -3.805 -0.451 0.744
8 C8 C C8 N Y N 0 -5.108 -0.206 0.282
9 C12 C C9 N Y N 0 -6.23 -0.561 1.051
10 C13 C C10 N Y N 0 -7.48 -0.308 0.574
11 C15 C C11 N Y N 0 -6.602 0.647 -1.442
12 C9 C C12 N Y N 0 -5.296 0.41 -0.981
13 C1' C C14 R N N 0 2.208 0.152 -0.285
14 C11 C C13 N Y N 0 -2.924 0.527 -1.287
15 N5 N N1 N Y N 0 -0.268 0.062 -0.21
16 S2 S S1 N Y N 0 0.669 -1.086 1.771
17 O5' O O1 N N N 0 3.089 -0.972 -0.223
18 C5' C C15 R N N 0 4.379 -0.733 -0.788
19 C6' C C16 N N N 0 5.222 -2.006 -0.692
20 O6' O O2 N N N 0 4.637 -3.027 -1.503
21 C4' C C17 S N N 0 5.071 0.396 -0.02
22 O4' O O3 N N N 0 6.338 0.675 -0.619
23 C3' C C18 S N N 0 4.192 1.65 -0.071
24 O3' O O4 N N N 0 4.795 2.688 0.706
25 C2' C C19 R N N 0 2.812 1.317 0.504
26 O2' O O5 N N N 0 1.961 2.459 0.395
27 H1 H H1 N N N 0 -1.812 -1.427 2.262
28 H2 H H2 N N N 0 -4.313 1.236 -2.718
29 H3 H H3 N N N 0 -8.667 0.486 -1.022
30 H4 H H4 N N N 0 -3.647 -0.92 1.704
31 H5 H H5 N N N 0 -6.102 -1.031 2.015
32 H6 H H6 N N N 0 -8.341 -0.582 1.166
33 H7 H H7 N N N 0 -6.761 1.11 -2.405
34 H8 H H8 N N N 0 -2.07 0.808 -1.885
35 H9 H H9 N N N 0 2.07 0.449 -1.324
36 H10 H H10 N N N 0 4.27 -0.447 -1.835
37 H11 H H11 N N N 0 6.234 -1.8 -1.041
38 H12 H H12 N N N 0 5.257 -2.341 0.345
39 H13 H H13 N N N 0 5.12 -3.865 -1.49
40 H14 H H14 N N N 0 5.216 0.095 1.017
41 H15 H H15 N N N 0 6.832 1.382 -0.182
42 H16 H H16 N N N 0 4.087 1.98 -1.104
43 H17 H H17 N N N 0 4.291 3.513 0.718
44 H19 H H19 N N N 0 1.069 2.319 0.74
45 H18 H H18 N N N 0 2.912 1.034 1.552



KVE : Chemical Bonds

Total Number of Bonds: 48
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3' C3' O C sing 1.43 N N
2 O4' C4' O C sing 1.43 N N
3 C3' C4' C C sing 1.53 N N
4 C3' C2' C C sing 1.53 N N
5 C4' C5' C C sing 1.53 N N
6 O2' C2' O C sing 1.43 N N
7 C2' C1' C C sing 1.53 N N
8 O6' C6' O C sing 1.43 N N
9 C5' C6' C C sing 1.53 N N
10 C5' O5' C O sing 1.43 N N
11 C1' O5' C O sing 1.43 N N
12 C1' C1 C C sing 1.51 N N
13 S2 C1 S C sing 1.71 N Y
14 S2 C3 S C sing 1.76 N Y
15 C1 N5 C N doub 1.29 N Y
16 C3 C4 C C doub 1.35 N Y
17 N5 C4 N C sing 1.32 N Y
18 C4 C6 C C sing 1.48 N N
19 C6 C7 C C doub 1.38 N Y
20 C6 C11 C C sing 1.4 N Y
21 C7 C8 C C sing 1.4 N Y
22 C11 C10 C C doub 1.36 N Y
23 C8 C12 C C doub 1.41 N Y
24 C8 C9 C C sing 1.42 N Y
25 C12 C13 C C sing 1.36 N Y
26 C10 C9 C C sing 1.41 N Y
27 C9 C15 C C doub 1.41 N Y
28 C13 C14 C C doub 1.39 N Y
29 C15 C14 C C sing 1.36 N Y
30 C3 H1 C H sing 1.08 N N
31 C10 H2 C H sing 1.08 N N
32 C14 H3 C H sing 1.08 N N
33 C7 H4 C H sing 1.08 N N
34 C12 H5 C H sing 1.08 N N
35 C13 H6 C H sing 1.08 N N
36 C15 H7 C H sing 1.08 N N
37 C11 H8 C H sing 1.08 N N
38 C1' H9 C H sing 1.09 N N
39 C5' H10 C H sing 1.09 N N
40 C6' H11 C H sing 1.09 N N
41 C6' H12 C H sing 1.09 N N
42 O6' H13 O H sing 0.97 N N
43 C4' H14 C H sing 1.09 N N
44 O4' H15 O H sing 0.97 N N
45 C3' H16 C H sing 1.09 N N
46 O3' H17 O H sing 0.97 N N
47 C2' H18 C H sing 1.09 N N
48 O2' H19 O H sing 0.97 N N



KVE : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
KVE 6s4p Open in New Window Bound ligand 1 1