Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

UI5 : Summary

Code

UI5

One-letter code

X

Molecule name

(1~{S},2~{S},3~{S},4~{R})-4-azanyl-3-(hydroxymethyl)cyclopentane-1,2-diol

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (1~{S},2~{S},3~{S},4~{R})-4-azanyl-3-(hydroxymethyl)cyclopentane-1,2-diol

Formula

C6 H13 N O3

Formal charge

0

Molecular weight

147.172 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 N[CH]1C[CH](O)[CH](O)[CH]1CO
SMILES OpenEye OEToolkits 2.0.7 C1C(C(C(C1O)O)CO)N
Canonical SMILES CACTVS 3.385 N[C@@H]1C[C@H](O)[C@@H](O)[C@@H]1CO
Canonical SMILES OpenEye OEToolkits 2.0.7 C1[C@H]([C@H]([C@@H]([C@H]1O)O)CO)N

IUPAC InChI

InChI=1S/C6H13NO3/c7-4-1-5(9)6(10)3(4)2-8/h3-6,8-10H,1-2,7H2/t3-,4-,5+,6+/m1/s1

IUPAC InChI key

XJKPQBOZNVQXOP-ZXXMMSQZSA-N
UI5

wwPDB Information

Atom count

23 (10 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-09-05

Last modified at

2023-12-08

Status

Released

Obsoleted

Not Assigned



UI5 : Atoms of Molecule

Total Number of Atoms: 23
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C6 C C1 N N N 0 2.043 0.325 0.197
2 C5 C C2 S N N 0 0.719 0.172 -0.555
3 C1 C C3 R N N 0 -0.06 1.503 -0.551
4 C2 C C4 N N N 0 -1.548 1.141 -0.396
5 C3 C C5 S N N 0 -1.62 -0.398 -0.311
6 O3 O O1 N N N 0 2.78 -0.897 0.117
7 C4 C C6 S N N 0 -0.213 -0.82 0.184
8 O2 O O2 N N N 0 0.074 -2.168 -0.194
9 N1 N N1 N N N 0 0.375 2.338 0.577
10 O1 O O3 N N N 0 -2.622 -0.801 0.625
11 H12 H H1 N N N 0 2.625 1.13 -0.252
12 H13 H H2 N N N 0 1.842 0.561 1.242
13 H11 H H3 N N N 0 0.899 -0.162 -1.577
14 H4 H H4 N N N 0 0.099 2.032 -1.491
15 H6 H H5 N N N 0 -1.947 1.584 0.517
16 H5 H H6 N N N 0 -2.111 1.494 -1.26
17 H7 H H7 N N N 0 -1.823 -0.825 -1.293
18 H14 H H8 N N N 0 3.632 -0.873 0.573
19 H9 H H9 N N N 0 -0.13 -0.697 1.264
20 H10 H H10 N N N 0 -0.534 -2.819 0.181
21 H1 H H11 N N N 0 -0.143 3.204 0.606
22 H2 H H12 N N N 0 0.293 1.838 1.449
23 H8 H H14 N N N 0 -3.515 -0.513 0.393



UI5 : Chemical Bonds

Total Number of Bonds: 23
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C1 N C sing 1.47 N N
2 C1 C2 C C sing 1.54 N N
3 C1 C5 C C sing 1.54 N N
4 C2 C3 C C sing 1.54 N N
5 C3 O1 C O sing 1.43 N N
6 C3 C4 C C sing 1.55 N N
7 C4 O2 C O sing 1.43 N N
8 C4 C5 C C sing 1.55 N N
9 C5 C6 C C sing 1.53 N N
10 C6 O3 C O sing 1.43 N N
11 C6 H12 C H sing 1.09 N N
12 C6 H13 C H sing 1.09 N N
13 C5 H11 C H sing 1.09 N N
14 C1 H4 C H sing 1.09 N N
15 C2 H6 C H sing 1.09 N N
16 C2 H5 C H sing 1.09 N N
17 C3 H7 C H sing 1.09 N N
18 O3 H14 O H sing 0.97 N N
19 C4 H9 C H sing 1.09 N N
20 O2 H10 O H sing 0.97 N N
21 N1 H1 N H sing 1.01 N N
22 N1 H2 N H sing 1.01 N N
23 O1 H8 O H sing 0.97 N N



UI5 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
UI5 8qf2 Open in New Window Bound ligand 1 1
UI5 8qf8 Open in New Window Bound ligand 1 1