Chemical Components in the PDB

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  • LXC (Stereoisomer)
  • HSY (Stereoisomer)
  • ARB (Stereoisomer)
  • ARA (Stereoisomer)
  • XYP (Stereoisomer)
  • 64K (Stereoisomer)
  • XYS (Stereoisomer)
  • 0MK (Stereoisomer)
  • LDY (Stereoisomer)

RIP : Summary

Code

RIP

One-letter code

X

Molecule name

RIBOSE(PYRANOSE FORM)

Systematic names

ProgramVersionName
ACDLabs 10.04 beta-D-ribopyranose
OpenEye OEToolkits 1.5.0 (2R,3R,4R,5R)-oxane-2,3,4,5-tetrol

Formula

C5 H10 O5

Formal charge

0

Molecular weight

150.13 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 OC1C(O)COC(O)C1O
SMILES CACTVS 3.341 O[CH]1CO[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 C1C(C(C(C(O1)O)O)O)O
Canonical SMILES CACTVS 3.341 O[C@@H]1CO[C@@H](O)[C@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 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-/m1/s1

IUPAC InChI key

SRBFZHDQGSBBOR-TXICZTDVSA-N
RIP

wwPDB Information

Atom count

20 (10 without Hydrogen)

Polymer type

Saccharide

Type description

SACCHARIDE

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



RIP : 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 R N N 0 0.538 0.292 -1.219
2 C2 C C2 R N N 0 -0.651 -0.575 -0.803
3 C3 C C3 R N N 0 -0.96 -0.326 0.677
4 C4 C C4 R N N 0 0.322 -0.541 1.489
5 C5 C C5 N N N 0 1.438 0.324 0.899
6 H1 H H1 N N N 0 0.298 1.342 -1.049
7 H2 H H2 N N N 0 -0.405 -1.627 -0.95
8 H3 H H3 N N N 0 -1.729 -1.022 1.013
9 H4 H H4 N N N 0 0.611 -1.591 1.442
10 H51 H 1H5 N N N 0 1.138 1.371 0.927
11 H52 H 2H5 N N N 0 2.347 0.192 1.486
12 HO1 H HO1 N N N 0 1.563 0.653 -2.829
13 HO2 H HO2 N N N 0 -1.551 -0.402 -2.516
14 HO3 H HO3 N N N 0 -1.601 1.128 1.795
15 HO4 H HO4 N N N 0 0.926 -0.315 3.322
16 O1 O O1 N N Y 0 0.812 0.086 -2.606
17 O2 O O2 N N N 0 -1.791 -0.235 -1.595
18 O3 O O3 N N N 0 -1.419 1.015 0.852
19 O4 O O4 N N N 0 0.095 -0.167 2.849
20 O5 O O5 N N N 0 1.686 -0.061 -0.45



RIP : 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 C1 C2 C C sing 1.53 N N
2 C1 O1 C O sing 1.43 N N
3 C1 O5 C O sing 1.43 N N
4 C1 H1 C H sing 1.09 N N
5 C2 C3 C C sing 1.53 N N
6 C2 O2 C O sing 1.43 N N
7 C2 H2 C H sing 1.09 N N
8 C3 C4 C C sing 1.53 N N
9 C3 O3 C O sing 1.43 N N
10 C3 H3 C H sing 1.09 N N
11 C4 C5 C C sing 1.53 N N
12 C4 O4 C O sing 1.43 N N
13 C4 H4 C H sing 1.09 N N
14 C5 O5 C O sing 1.42 N N
15 C5 H51 C H sing 1.09 N N
16 C5 H52 C H sing 1.09 N N
17 O1 HO1 O H sing 0.97 N N
18 O2 HO2 O H sing 0.97 N N
19 O3 HO3 O H sing 0.97 N N
20 O4 HO4 O H sing 0.97 N N



RIP : Used in PDB Entries

Total Number of PDB Entries: 16
Ligand Code PDB Entry ID Type Total Distinct
RIP 1a7c Open in New Window Bound ligand 1 1
RIP 1dbp Open in New Window Bound ligand 1 1
RIP 1drj Open in New Window Bound ligand 1 1
RIP 1drk Open in New Window Bound ligand 1 1
RIP 1ogd Open in New Window Bound ligand 5 1
RIP 1y7p Open in New Window Bound ligand 3 1
RIP 2dri Open in New Window Bound ligand 1 1
RIP 2fn8 Open in New Window Bound ligand 1 1
RIP 2gx6 Open in New Window Bound ligand 1 1
RIP 2ioy Open in New Window Bound ligand 2 1
RIP 2px1 Open in New Window Bound ligand 2 1
RIP 3n1d Open in New Window Bound ligand 1 1
RIP 3p13 Open in New Window Bound ligand 4 1
RIP 3sj6 Open in New Window Bound ligand 1 1
RIP 4ry0 Open in New Window Bound ligand 1 1
RIP 4zjp Open in New Window Bound ligand 1 1