Chemical Components in the PDB

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NBV : Summary

Code

NBV

One-letter code

X

Molecule name

(2R,3R,4R,5S)-1-BUTYL-2-(HYDROXYMETHYL)PIPERIDINE-3,4,5-TRIOL

Systematic names

ProgramVersionName
ACDLabs 10.04 (2R,3R,4R,5S)-1-butyl-2-(hydroxymethyl)piperidine-3,4,5-triol
OpenEye OEToolkits 1.5.0 (1R,2R,3R,4R,5S)-1-butyl-2-(hydroxymethyl)piperidine-3,4,5-triol

Formula

C10 H21 N O4

Formal charge

0

Molecular weight

219.278 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 OCC1N(CCCC)CC(O)C(O)C1O
SMILES CACTVS 3.341 CCCCN1C[CH](O)[CH](O)[CH](O)[CH]1CO
SMILES OpenEye OEToolkits 1.5.0 CCCCN1CC(C(C(C1CO)O)O)O
Canonical SMILES CACTVS 3.341 CCCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO
Canonical SMILES OpenEye OEToolkits 1.5.0 CCCC[N@@]1C[C@@H]([C@H]([C@@H]([C@H]1CO)O)O)O

IUPAC InChI

InChI=1S/C10H21NO4/c1-2-3-4-11-5-8(13)10(15)9(14)7(11)6-12/h7-10,12-15H,2-6H2,1H3/t7-,8+,9-,10-/m1/s1

IUPAC InChI key

UQRORFVVSGFNRO-UTINFBMNSA-N
NBV

wwPDB Information

Atom count

36 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2007-06-18

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



NBV : Atoms of Molecule

Total Number of Atoms: 36
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O9 O O9 N N N 0 -0.134 2.682 1.114
2 C12 C C12 N N N 0 -0.154 2.463 -0.298
3 C11 C C11 R N N 0 -0.547 1.013 -0.584
4 C10 C C10 R N N 0 -1.898 0.711 0.07
5 O1 O O1 N N N 0 -2.896 1.574 -0.479
6 C9 C C9 R N N 0 -2.277 -0.747 -0.202
7 O8 O O8 N N N 0 -3.51 -1.05 0.453
8 C8 C C8 S N N 0 -1.174 -1.662 0.336
9 O7 O O7 N N N 0 -1.493 -3.022 0.036
10 N1 N N1 N N N 0 0.475 0.112 -0.035
11 C7 C C7 N N N 0 0.156 -1.292 -0.326
12 C13 C C13 N N N 0 1.81 0.463 -0.537
13 C14 C C14 N N N 0 2.864 -0.377 0.186
14 C15 C C15 N N N 0 4.255 -0.012 -0.336
15 C16 C C16 N N N 0 5.309 -0.852 0.388
16 H9 H H9 N N N 0 0.108 3.582 1.37
17 H121 H 1H12 N N N 0 -0.88 3.134 -0.758
18 H122 H 2H12 N N N 0 0.835 2.66 -0.71
19 H11 H H11 N N N 0 -0.623 0.862 -1.661
20 H10 H H10 N N N 0 -1.827 0.875 1.145
21 H1 H H1 N N N 0 -3.779 1.439 -0.11
22 HA H HA N N N 0 -2.388 -0.9 -1.276
23 H8 H H8 N N N 0 -3.812 -1.959 0.324
24 HB H HB N N N 0 -1.091 -1.537 1.415
25 H7 H H7 N N N 0 -0.836 -3.659 0.348
26 H7C1 H 1H7C N N N 0 0.947 -1.932 0.066
27 H7C2 H 2H7C N N N 0 0.077 -1.431 -1.404
28 H131 H 1H13 N N N 0 1.86 0.265 -1.608
29 H132 H 2H13 N N N 0 2.0 1.521 -0.354
30 H141 H 1H14 N N N 0 2.815 -0.179 1.257
31 H142 H 2H14 N N N 0 2.674 -1.435 0.0040
32 H151 H 1H15 N N N 0 4.304 -0.21 -1.407
33 H152 H 2H15 N N N 0 4.445 1.046 -0.153
34 H161 H 1H16 N N N 0 5.119 -1.909 0.205
35 H162 H 2H16 N N N 0 6.3 -0.591 0.015
36 H163 H 3H16 N N N 0 5.259 -0.654 1.458



NBV : Chemical Bonds

Total Number of Bonds: 36
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O9 C12 O C sing 1.43 N N
2 O9 H9 O H sing 0.97 N N
3 C12 C11 C C sing 1.53 N N
4 C12 H121 C H sing 1.09 N N
5 C12 H122 C H sing 1.09 N N
6 C11 C10 C C sing 1.53 N N
7 C11 N1 C N sing 1.47 N N
8 C11 H11 C H sing 1.09 N N
9 C10 O1 C O sing 1.43 N N
10 C10 C9 C C sing 1.53 N N
11 C10 H10 C H sing 1.09 N N
12 O1 H1 O H sing 0.97 N N
13 C9 O8 C O sing 1.43 N N
14 C9 C8 C C sing 1.53 N N
15 C9 HA C H sing 1.09 N N
16 O8 H8 O H sing 0.97 N N
17 C8 O7 C O sing 1.43 N N
18 C8 C7 C C sing 1.53 N N
19 C8 HB C H sing 1.09 N N
20 O7 H7 O H sing 0.97 N N
21 N1 C7 N C sing 1.47 N N
22 N1 C13 N C sing 1.47 N N
23 C7 H7C1 C H sing 1.09 N N
24 C7 H7C2 C H sing 1.09 N N
25 C13 C14 C C sing 1.53 N N
26 C13 H131 C H sing 1.09 N N
27 C13 H132 C H sing 1.09 N N
28 C14 C15 C C sing 1.53 N N
29 C14 H141 C H sing 1.09 N N
30 C14 H142 C H sing 1.09 N N
31 C15 C16 C C sing 1.53 N N
32 C15 H151 C H sing 1.09 N N
33 C15 H152 C H sing 1.09 N N
34 C16 H161 C H sing 1.09 N N
35 C16 H162 C H sing 1.09 N N
36 C16 H163 C H sing 1.09 N N



NBV : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
NBV 2v3d Open in New Window Bound ligand 2 1
NBV 5ief Open in New Window Bound ligand 1 1