Chemical Components in the PDB

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R1P : Summary

Code

R1P

One-letter code

X

Molecule name

1-O-phosphono-alpha-D-ribofuranose

Synonyms

RIBOSE-1-PHOSPHATE
1-O-phosphono-alpha-D-ribose
1-O-phosphono-D-ribose
1-O-phosphono-ribose

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

D-saccharide, alpha linking

Type code

ATOMS

Is modified

Yes

Standard parent

RIB

Defined at

1999-07-08

Last modified at

2020-07-17

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 C5 C C5' N N N 0 1.695 -0.423 2.674
2 O5 O O5' N N N 0 2.859 0.374 2.453
3 C4 C C4' R N N 0 0.473 0.283 2.084
4 O4 O O4' N N N 0 0.639 0.442 0.67
5 C1 C C1' R N N 0 -0.389 -0.276 -0.028
6 C2 C C2' R N N 0 -1.562 -0.385 0.978
7 O2 O O2' N N N 0 -2.337 0.815 0.997
8 C3 C C3' S N N 0 -0.789 -0.574 2.314
9 O3 O O3' N N N 0 -1.553 -0.081 3.417
10 O1 O O1' N N N 0 -0.796 0.446 -1.191
11 P P P N N N 0 0.118 -0.076 -2.408
12 O1P O O1P N N N 0 -0.089 -1.529 -2.593
13 O2P O O2P N N N 0 -0.289 0.7 -3.758
14 O3P O O3P N N N 0 1.668 0.206 -2.074
15 H51 H H5'1 N N N 0 1.822 -1.392 2.192
16 H52 H H5'2 N N N 0 1.55 -0.566 3.745
17 HO5 H HO5' N N Y 0 3.605 -0.105 2.839
18 H4 H H4' N N N 0 0.348 1.259 2.554
19 H1 H H1' N N N 0 -0.035 -1.269 -0.305
20 H2 H H2' N N N 0 -2.188 -1.25 0.76
21 HO2 H HO2' N N Y 0 -2.698 0.928 0.108
22 H3 H H3' N N N 0 -0.524 -1.62 2.464
23 HO3 H HO3' N N Y 0 -2.366 -0.603 3.448
24 HOP2 H HOP2 N N N 0 0.281 0.359 -4.46
25 HOP3 H HOP3 N N N 0 1.76 1.161 -1.961



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 H51 C H sing 1.09 N N
4 C5 H52 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: 10
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
R1P 6k8p Open in New Window Bound ligand 2 1