Chemical Components in the PDB

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KV5 : Summary

Code

KV5

One-letter code

X

Molecule name

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

Systematic names

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

Formula

C19 H20 N2 O5

Formal charge

0

Molecular weight

356.373 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)c2c[nH]c(n2)c3ccc4ccccc4c3
SMILES OpenEye OEToolkits 2.0.7 c1ccc2cc(ccc2c1)c3[nH]cc(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)c2c[nH]c(n2)c3ccc4ccccc4c3
Canonical SMILES OpenEye OEToolkits 2.0.7 c1ccc2cc(ccc2c1)c3[nH]cc(n3)[C@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O

IUPAC InChI

InChI=1S/C19H20N2O5/c22-9-14-15(23)16(24)17(25)18(26-14)13-8-20-19(21-13)12-6-5-10-3-1-2-4-11(10)7-12/h1-8,14-18,22-25H,9H2,(H,20,21)/t14-,15-,16+,17-,18+/m1/s1

IUPAC InChI key

VRUXFQSZTNCMBM-SFFUCWETSA-N
KV5

wwPDB Information

Atom count

46 (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



KV5 : Atoms of Molecule

Total Number of Atoms: 46
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N Y N 0 -1.188 1.397 -0.047
2 C6 C C2 N Y N 0 -2.583 0.91 -0.076
3 C8 C C3 N Y N 0 -4.166 -0.904 -0.02
4 N3 N N1 N Y N 0 -0.795 2.702 -0.116
5 C2' C C8 R N N 0 2.57 0.089 1.392
6 C2 C C4 N Y N 0 0.572 2.712 -0.056
7 O5' O O1 N N N 0 2.725 0.185 -1.018
8 C5' C C5 R N N 0 4.071 -0.293 -1.043
9 C4' C C6 S N N 0 4.308 -1.21 0.161
10 C3' C C7 R N N 0 4.007 -0.437 1.448
11 C1' C C9 S N N 0 2.401 0.956 0.141
12 C1 C C10 N Y N 0 0.973 1.428 0.047
13 N5 N N2 N Y N 0 -0.113 0.647 0.055
14 O2' O O2 N N N 0 2.302 0.873 2.556
15 O3' O O3 N N N 0 4.154 -1.306 2.573
16 O4' O O4 N N N 0 5.669 -1.645 0.17
17 C6' C C11 N N N 0 4.311 -1.076 -2.335
18 O6' O O5 N N N 0 4.204 -0.193 -3.454
19 C11 C C12 N Y N 0 -3.641 1.829 -0.188
20 C10 C C13 N Y N 0 -4.931 1.407 -0.216
21 C9 C C14 N Y N 0 -5.224 0.034 -0.133
22 C7 C C15 N Y N 0 -2.839 -0.449 0.003
23 C15 C C16 N Y N 0 -6.55 -0.427 -0.155
24 C14 C C17 N Y N 0 -6.803 -1.762 -0.068
25 C13 C C18 N Y N 0 -5.764 -2.684 0.044
26 C12 C C19 N Y N 0 -4.465 -2.275 0.069
27 H1 H H1 N N N 0 -1.376 3.475 -0.193
28 H2 H H2 N N N 0 1.209 3.583 -0.089
29 H4 H H4 N N N 0 3.649 -2.076 0.094
30 H3 H H3 N N N 0 4.758 0.552 -0.996
31 H5 H H5 N N N 0 4.699 0.401 1.54
32 H6 H H6 N N N 0 1.876 -0.751 1.35
33 H7 H H7 N N N 0 3.066 1.817 0.203
34 H9 H H9 N N N 0 2.395 0.388 3.387
35 H10 H H10 N N N 0 3.979 -0.881 3.424
36 H11 H H11 N N N 0 5.89 -2.23 0.907
37 H15 H H15 N N N 0 -3.424 2.885 -0.253
38 H12 H H12 N N N 0 5.309 -1.515 -2.314
39 H13 H H13 N N N 0 3.567 -1.867 -2.424
40 H14 H H14 N N N 0 4.345 -0.622 -4.309
41 H16 H H16 N N N 0 -5.732 2.126 -0.303
42 H20 H H20 N N N 0 -5.991 -3.737 0.112
43 H17 H H17 N N N 0 -2.023 -1.152 0.084
44 H18 H H18 N N N 0 -7.367 0.275 -0.241
45 H19 H H19 N N N 0 -7.824 -2.112 -0.086
46 H21 H H21 N N N 0 -3.67 -3.0 0.155



KV5 : Chemical Bonds

Total Number of Bonds: 49
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 C2 C1 C C doub 1.35 N Y
14 C2 N3 C N sing 1.37 N Y
15 C1 N5 C N sing 1.34 N Y
16 N3 C4 N C sing 1.36 N Y
17 N5 C4 N C doub 1.31 N Y
18 C4 C6 C C sing 1.48 N N
19 C6 C7 C C doub 1.39 N Y
20 C6 C11 C C sing 1.41 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 1.4 N Y
28 C13 C14 C C doub 1.39 N Y
29 C15 C14 C C sing 1.36 N Y
30 N3 H1 N H sing 0.97 N N
31 C2 H2 C H sing 1.08 N N
32 C5' H3 C H sing 1.09 N N
33 C4' H4 C H sing 1.09 N N
34 C3' H5 C H sing 1.09 N N
35 C2' H6 C H sing 1.09 N N
36 C1' H7 C H sing 1.09 N N
37 O2' H9 O H sing 0.97 N N
38 O3' H10 O H sing 0.97 N N
39 O4' H11 O H sing 0.97 N N
40 C6' H12 C H sing 1.09 N N
41 C6' H13 C H sing 1.09 N N
42 O6' H14 O H sing 0.97 N N
43 C11 H15 C H sing 1.08 N N
44 C10 H16 C H sing 1.08 N N
45 C7 H17 C H sing 1.08 N N
46 C15 H18 C H sing 1.08 N N
47 C14 H19 C H sing 1.08 N N
48 C13 H20 C H sing 1.08 N N
49 C12 H21 C H sing 1.08 N N



KV5 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
KV5 6s4o Open in New Window Bound ligand 1 1