Chemical Components in the PDB

pdbe.org/chem
spacer

R1P : Summary

Code

R1P

One-letter code

X

Molecule name

RIBOSE-1-PHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 1-O-phosphono-alpha-D-ribofuranose
OpenEye OEToolkits 1.5.0 [(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl] dihydrogen phosphate

Formula

C5 H11 O8 P

Formal charge

0

Molecular weight

230.11 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(OC1OC(C(O)C1O)CO)(O)O
SMILES CACTVS 3.341 OC[CH]1O[CH](O[P](O)(O)=O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 C(C1C(C(C(O1)OP(=O)(O)O)O)O)O
Canonical SMILES CACTVS 3.341 OC[C@H]1O[C@H](O[P](O)(O)=O)[C@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 C([C@@H]1[C@H]([C@H]([C@H](O1)OP(=O)(O)O)O)O)O

IUPAC InChI

InChI=1S/C5H11O8P/c6-1-2-3(7)4(8)5(12-2)13-14(9,10)11/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1

IUPAC InChI key

YXJDFQJKERBOBM-TXICZTDVSA-N
R1P

wwPDB Information

Atom count

25 (14 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



R1P : Atoms of Molecule

Total Number of Atoms: 25
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 -0.389 -0.276 -0.028
2 C2' C C2' R N N 0 -1.562 -0.385 0.978
3 C3' C C3' S N N 0 -0.789 -0.574 2.314
4 C4' C C4' R N N 0 0.473 0.283 2.084
5 C5' C C5' N N N 0 1.695 -0.423 2.674
6 H1' H H1' N N N 0 -0.035 -1.269 -0.305
7 H2' H H2' N N N 0 -2.188 -1.25 0.76
8 H3' H H3' N N N 0 -0.524 -1.62 2.464
9 H4' H H4' N N N 0 0.348 1.259 2.554
10 H5'1 H 1H5' N N N 0 1.822 -1.392 2.192
11 H5'2 H 2H5' N N N 0 1.55 -0.566 3.745
12 HO2' H 'HO2 N N N 0 -2.698 0.928 0.108
13 HO3' H 'HO3 N N N 0 -2.366 -0.603 3.448
14 HO5' H 'HO5 N N N 0 3.605 -0.105 2.839
15 HOP2 H 2HOP N N N 0 0.281 0.359 -4.46
16 HOP3 H 3HOP N N N 0 1.76 1.161 -1.961
17 O1' O O1' N N N 0 -0.796 0.446 -1.191
18 O1P O O1P N N N 0 -0.089 -1.529 -2.593
19 O2' O O2' N N N 0 -2.337 0.815 0.997
20 O2P O O2P N N N 0 -0.289 0.7 -3.758
21 O3' O O3' N N N 0 -1.553 -0.081 3.417
22 O3P O O3P N N N 0 1.668 0.206 -2.074
23 O4' O O4' N N N 0 0.639 0.442 0.67
24 O5' O O5' N N N 0 2.859 0.374 2.453
25 P P P N N N 0 0.118 -0.076 -2.408



R1P : Chemical Bonds

Total Number of Bonds: 25
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C5' O5' C O sing 1.43 N N
2 C5' C4' C C sing 1.53 N N
3 C5' H5'1 C H sing 1.09 N N
4 C5' H5'2 C H sing 1.09 N N
5 O5' HO5' O H sing 0.97 N N
6 C4' O4' C O sing 1.43 N N
7 C4' C3' C C sing 1.54 N N
8 C4' H4' C H sing 1.09 N N
9 O4' C1' O C sing 1.44 N N
10 C1' C2' C C sing 1.55 N N
11 C1' O1' C O sing 1.43 N N
12 C1' H1' C H sing 1.09 N N
13 C2' O2' C O sing 1.43 N N
14 C2' C3' C C sing 1.56 N N
15 C2' H2' C H sing 1.09 N N
16 O2' HO2' O H sing 0.97 N N
17 C3' O3' C O sing 1.43 N N
18 C3' H3' C H sing 1.09 N N
19 O3' HO3' O H sing 0.97 N N
20 O1' P O P sing 1.61 N N
21 P O1P P O doub 1.48 N N
22 P O2P P O sing 1.61 N N
23 P O3P P O sing 1.61 N N
24 O2P HOP2 O H sing 0.97 N N
25 O3P HOP3 O H sing 0.97 N N



R1P : Used in PDB Entries

Total Number of PDB Entries: 9
Ligand Code PDB Entry ID Type Total Distinct
R1P 1a9t Open in New Window Bound ligand 1 1
R1P 1rxc Open in New Window Bound ligand 8 1
R1P 1tgy Open in New Window Bound ligand 2 1
R1P 2h4l Open in New Window Bound ligand 1 1
R1P 3bje Open in New Window Bound ligand 2 1
R1P 3fb1 Open in New Window Bound ligand 3 1
R1P 3qpb Open in New Window Bound ligand 18 1
R1P 5ko6 Open in New Window Bound ligand 1 1
R1P 6k5h Open in New Window Bound ligand 4 1