Chemical Components in the PDB

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IMR : Summary

Code

IMR

One-letter code

X

Molecule name

IMINORIBITOL

Systematic names

ProgramVersionName
ACDLabs 10.04 (2R,3R,4S)-2-(hydroxymethyl)pyrrolidine-3,4-diol
OpenEye OEToolkits 1.5.0 (2R,3R,4S)-2-(hydroxymethyl)pyrrolidine-3,4-diol

Formula

C5 H11 N O3

Formal charge

0

Molecular weight

133.146 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 OCC1NCC(O)C1O
SMILES CACTVS 3.341 OC[CH]1NC[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 C1C(C(C(N1)CO)O)O
Canonical SMILES CACTVS 3.341 OC[C@H]1NC[C@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1[C@@H]([C@@H]([C@H](N1)CO)O)O

IUPAC InChI

InChI=1S/C5H11NO3/c7-2-3-5(9)4(8)1-6-3/h3-9H,1-2H2/t3-,4+,5-/m1/s1

IUPAC InChI key

OQEBIHBLFRADNM-MROZADKFSA-N
IMR

wwPDB Information

Atom count

20 (9 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2001-03-29

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



IMR : Atoms of Molecule

Total Number of Atoms: 20
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O5' O O5* N N N 0 -0.068 -0.017 3.19
2 C5' C C5* N N N 0 0.532 0.537 2.019
3 C4' C C4* R N N 0 0.165 -0.317 0.803
4 N4' N N4* N N N 0 -1.3 -0.308 0.606
5 C3' C C3* R N N 0 0.8 0.277 -0.466
6 O3' O O3* N N N 0 1.673 -0.669 -1.084
7 C2' C C2* S N N 0 -0.396 0.594 -1.4
8 O2' O O2* N N N 0 -0.079 0.276 -2.756
9 C1' C C1* N N N 0 -1.511 -0.337 -0.863
10 HO'5 H 5HO* N N N 0 0.187 0.549 3.931
11 H5'1 H 1H5* N N N 0 0.169 1.554 1.871
12 H5'2 H 2H5* N N N 0 1.616 0.552 2.138
13 H4' H H4* N N N 0 0.514 -1.339 0.949
14 HN'4 H 4HN* N N N 0 -1.646 -1.185 0.966
15 H3' H H3* N N N 0 1.344 1.191 -0.225
16 HO'3 H 3HO* N N N 0 2.003 -0.259 -1.895
17 H2' H H2* N N N 0 -0.691 1.64 -1.309
18 HO'2 H 2HO* N N N 0 -0.885 0.418 -3.272
19 H1'1 H 1H1* N N N 0 -2.495 0.053 -1.118
20 H1'2 H 2H1* N N N 0 -1.385 -1.349 -1.25



IMR : Chemical Bonds

Total Number of Bonds: 20
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O5' C5' O C sing 1.43 N N
2 O5' HO'5 O H sing 0.97 N N
3 C5' C4' C C sing 1.53 N N
4 C5' H5'1 C H sing 1.09 N N
5 C5' H5'2 C H sing 1.09 N N
6 C4' N4' C N sing 1.48 N N
7 C4' C3' C C sing 1.54 N N
8 C4' H4' C H sing 1.09 N N
9 N4' C1' N C sing 1.48 N N
10 N4' HN'4 N H sing 1.01 N N
11 C3' O3' C O sing 1.43 N N
12 C3' C2' C C sing 1.55 N N
13 C3' H3' C H sing 1.09 N N
14 O3' HO'3 O H sing 0.97 N N
15 C2' O2' C O sing 1.43 N N
16 C2' C1' C C sing 1.55 N N
17 C2' H2' C H sing 1.09 N N
18 O2' HO'2 O H sing 0.97 N N
19 C1' H1'1 C H sing 1.09 N N
20 C1' H1'2 C H sing 1.09 N N



IMR : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
IMR 1i80 Open in New Window Bound ligand 1 1