Chemical Components in the PDB

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  • ARA (Stereoisomer)
  • ARB (Stereoisomer)
  • HSY (Stereoisomer)
  • LXC (Stereoisomer)
  • LDY (Stereoisomer)
  • RIP (Stereoisomer)
  • XYP (Stereoisomer)
  • XYS (Stereoisomer)

0MK : Summary

Code

0MK

One-letter code

X

Molecule name

L-ribopyranose

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.7.6 (2S,3S,4S,5S)-oxane-2,3,4,5-tetrol

Formula

C5 H10 O5

Formal charge

0

Molecular weight

150.13 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.370 O[CH]1CO[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.7.6 C1C(C(C(C(O1)O)O)O)O
Canonical SMILES CACTVS 3.370 O[C@H]1CO[C@H](O)[C@@H](O)[C@H]1O
Canonical SMILES OpenEye OEToolkits 1.7.6 C1[C@@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O

IUPAC InChI

InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3-,4-,5-/m0/s1

IUPAC InChI key

SRBFZHDQGSBBOR-FCAWWPLPSA-N
0MK

wwPDB Information

Atom count

20 (10 without Hydrogen)

Polymer type

Saccharide

Type description

L-SACCHARIDE

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2012-03-01

Last modified at

2013-03-15

Status

Released

Obsoleted

Not Assigned



0MK : 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 C1 C C1 S N N 0 -1.251 -0.532 0.302
2 C2 C C2 S N N 0 -0.814 0.652 -0.565
3 C3 C C3 S N N 0 0.661 0.959 -0.289
4 C4 C C4 S N N 0 1.493 -0.298 -0.561
5 C5 C C5 N N N 0 0.966 -1.446 0.306
6 H1 H H1 N N N 0 -1.16 -0.265 1.355
7 H10 H H10 N N N 0 3.446 -0.802 -0.381
8 H2 H H2 N N N 0 -0.944 0.401 -1.617
9 H3 H H3 N N N 0 0.994 1.766 -0.942
10 H4 H H4 N N N 0 1.41 -0.569 -1.613
11 H5 H H5 N N N 0 1.527 -2.354 0.085
12 H6 H H6 N N N 0 1.086 -1.191 1.359
13 H7 H H7 N N N 0 -2.955 -1.604 0.522
14 H8 H H8 N N N 0 -2.555 1.671 -0.391
15 H9 H H9 N N N 0 1.732 1.562 1.321
16 O1 O O1 N N N 0 -2.611 -0.86 0.0090
17 O2 O O2 N N N 0 -1.608 1.797 -0.245
18 O3 O O3 N N N 0 0.821 1.352 1.076
19 O4 O O4 N N N 0 2.861 -0.045 -0.237
20 O5 O O5 N N N 0 -0.418 -1.659 0.022



0MK : 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 O4 C4 O C sing 1.43 N N
2 C4 C5 C C sing 1.53 N N
3 C4 C3 C C sing 1.53 N N
4 C5 O5 C O sing 1.43 N N
5 C3 O3 C O sing 1.43 N N
6 C3 C2 C C sing 1.53 N N
7 O5 C1 O C sing 1.43 N N
8 C2 C1 C C sing 1.53 N N
9 C2 O2 C O sing 1.43 N N
10 C1 O1 C O sing 1.43 N N
11 C1 H1 C H sing 1.09 N N
12 C2 H2 C H sing 1.09 N N
13 C3 H3 C H sing 1.09 N N
14 C4 H4 C H sing 1.09 N N
15 C5 H5 C H sing 1.09 N N
16 C5 H6 C H sing 1.09 N N
17 O1 H7 O H sing 0.97 N N
18 O2 H8 O H sing 0.97 N N
19 O3 H9 O H sing 0.97 N N
20 O4 H10 O H sing 0.97 N N



0MK : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
0MK 4dux Open in New Window Bound ligand 9 1
0MK 4q0p Open in New Window Bound ligand 2 1
0MK 4q0u Open in New Window Bound ligand 1 1