Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

V71 : Summary

Code

V71

One-letter code

X

Molecule name

(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranoside

Systematic names

ProgramVersionName
ACDLabs 12.01 (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranoside
OpenEye OEToolkits 1.9.2 (1S,2R,3R,4S,6R)-3-[(2S,3R,4R,5R,6R)-6-(aminomethyl)-3-azanyl-5-fluoranyl-4-oxidanyl-oxan-2-yl]oxy-4,6-bis(azanyl)cyclo hexane-1,2-diol

Formula

C12 H25 F N4 O5

Formal charge

0

Molecular weight

324.349 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C1(C(C(O)C(C(CN)O1)F)N)OC2C(C(O)C(N)CC2N)O
SMILES CACTVS 3.385 NC[CH]1O[CH](O[CH]2[CH](N)C[CH](N)[CH](O)[CH]2O)[CH](N)[CH](O)[CH]1F
SMILES OpenEye OEToolkits 1.9.2 C1C(C(C(C(C1N)OC2C(C(C(C(O2)CN)F)O)N)O)O)N
Canonical SMILES CACTVS 3.385 NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O)[C@H]2O)[C@H](N)[C@@H](O)[C@H]1F
Canonical SMILES OpenEye OEToolkits 1.9.2 C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@@H]([C@H]([C@H]([C@H](O2)CN)F)O)N)O)O)N

IUPAC InChI

InChI=1S/C12H25FN4O5/c13-6-5(2-14)21-12(7(17)9(6)19)22-11-4(16)1-3(15)8(18)10(11)20/h3-12,18-20H,1-2,14-17H2/t3-,4+,5-,6+,7-,8+,9+,10-,11-,12-/m1/s1

IUPAC InChI key

CRXNRBKQEXVRGM-RMDUJVAESA-N
V71

wwPDB Information

Atom count

47 (22 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2015-06-17

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



V71 : Atoms of Molecule

Total Number of Atoms: 47
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 S N N 0 -0.953 0.779 -0.628
2 C10 C C10 R N N 0 1.186 -0.013 0.11
3 C11 C C11 R N N 0 2.176 1.113 -0.192
4 C12 C C12 S N N 0 3.527 0.513 -0.585
5 C2 C C2 R N N 0 -2.127 1.65 -0.175
6 C3 C C3 R N N 0 -2.922 0.901 0.9
7 C4 C C4 R N N 0 -3.382 -0.446 0.335
8 C7 C C7 R N N 0 4.061 -0.339 0.568
9 C5 C C5 R N N 0 -2.159 -1.236 -0.139
10 C6 C C6 N N N 0 -2.614 -2.558 -0.76
11 C8 C C8 N N N 0 3.071 -1.466 0.87
12 C9 C C9 S N N 0 1.719 -0.866 1.263
13 F99 F F99 N N N 0 -4.246 -0.23 -0.744
14 N2 N N2 N N N 0 -1.618 2.911 0.38
15 N6 N N6 N N N 0 -1.438 -3.367 -1.105
16 N7 N N7 N N N 0 5.359 -0.916 0.191
17 N9 N N9 N N N 0 0.769 -1.947 1.553
18 O1 O O1 N N N 0 -0.076 0.547 0.477
19 O11 O O11 N N N 0 1.677 1.909 -1.269
20 O12 O O12 N N N 0 4.452 1.565 -0.867
21 O3 O O23 N N N 0 -4.062 1.676 1.277
22 O5 O O5 N N N 0 -1.448 -0.471 -1.114
23 H1 H H1 N N N 0 -0.408 1.288 -1.423
24 H2A H H2 N N N 0 1.063 -0.637 -0.776
25 H3A H H3 N N N 0 2.299 1.736 0.693
26 H4A H H4 N N N 0 3.404 -0.11 -1.471
27 H2 H H5 N N N 0 -2.775 1.86 -1.026
28 H3 H H6 N N N 0 -2.29 0.736 1.772
29 H4 H H7 N N N 0 -3.901 -1.008 1.11
30 H5 H H8 N N N 0 -1.506 -1.439 0.71
31 H61 H H9 N N N 0 -3.232 -3.101 -0.045
32 H62 H H10 N N N 0 -3.193 -2.355 -1.661
33 H11 H H11 N N N 0 4.184 0.284 1.454
34 H12 H H12 N N N 0 2.948 -2.089 -0.016
35 H13 H H13 N N N 0 3.451 -2.073 1.692
36 H14 H H14 N N N 0 1.842 -0.243 2.149
37 H15 H H15 N N N 0 -2.375 3.503 0.687
38 H16 H H16 N N N 0 -0.967 2.738 1.132
39 H18 H H18 N N N 0 -1.712 -4.247 -1.517
40 H19 H H19 N N N 0 -0.816 -2.86 -1.716
41 H21 H H21 N N N 0 5.732 -1.484 0.937
42 H22 H H22 N N N 0 5.284 -1.446 -0.665
43 H24 H H24 N N N 0 1.146 -2.587 2.236
44 H25 H H25 N N N 0 -0.119 -1.577 1.856
45 H27 H H27 N N N 0 2.255 2.644 -1.515
46 H28 H H28 N N N 0 4.177 2.147 -1.59
47 HO3 H H29 N N Y 0 -4.613 1.261 1.956



V71 : 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 N6 C6 N C sing 1.47 N N
2 C6 C5 C C sing 1.53 N N
3 F99 C4 F C sing 1.4 N N
4 O5 C5 O C sing 1.43 N N
5 O5 C1 O C sing 1.43 N N
6 C5 C4 C C sing 1.53 N N
7 C4 C3 C C sing 1.53 N N
8 C1 C2 C C sing 1.53 N N
9 C1 O1 C O sing 1.43 N N
10 C2 C3 C C sing 1.53 N N
11 C2 N2 C N sing 1.47 N N
12 O11 C11 O C sing 1.43 N N
13 C3 O3 C O sing 1.43 N N
14 O1 C10 O C sing 1.43 N N
15 C10 C11 C C sing 1.53 N N
16 C10 C9 C C sing 1.53 N N
17 N9 C9 N C sing 1.47 N N
18 C11 C12 C C sing 1.53 N N
19 C12 O12 C O sing 1.43 N N
20 C12 C7 C C sing 1.53 N N
21 C9 C8 C C sing 1.53 N N
22 C8 C7 C C sing 1.53 N N
23 C7 N7 C N sing 1.47 N N
24 C1 H1 C H sing 1.09 N N
25 C10 H2A C H sing 1.09 N N
26 C11 H3A C H sing 1.09 N N
27 C12 H4A C H sing 1.09 N N
28 C2 H2 C H sing 1.09 N N
29 C3 H3 C H sing 1.09 N N
30 C4 H4 C H sing 1.09 N N
31 C5 H5 C H sing 1.09 N N
32 C6 H61 C H sing 1.09 N N
33 C6 H62 C H sing 1.09 N N
34 C7 H11 C H sing 1.09 N N
35 C8 H12 C H sing 1.09 N N
36 C8 H13 C H sing 1.09 N N
37 C9 H14 C H sing 1.09 N N
38 N2 H15 N H sing 1.01 N N
39 N2 H16 N H sing 1.01 N N
40 N6 H18 N H sing 1.01 N N
41 N6 H19 N H sing 1.01 N N
42 N7 H21 N H sing 1.01 N N
43 N7 H22 N H sing 1.01 N N
44 N9 H24 N H sing 1.01 N N
45 N9 H25 N H sing 1.01 N N
46 O11 H27 O H sing 0.97 N N
47 O12 H28 O H sing 0.97 N N
48 O3 HO3 O H sing 0.97 N N



V71 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
V71 6jbf Open in New Window Bound ligand 1 1