Chemical Components in the PDB

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PRP : Summary

Code

PRP

One-letter code

X

Molecule name

1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose

Systematic names

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

Formula

C5 H13 O14 P3

Formal charge

0

Molecular weight

390.07 Da

SMILES

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

IUPAC InChI

InChI=1S/C5H13O14P3/c6-3-2(1-16-20(8,9)10)17-5(4(3)7)18-22(14,15)19-21(11,12)13/h2-7H,1H2,(H,14,15)(H2,8,9,10)(H2,11,12,13)/t2-,3-,4-,5-/m1/s1

IUPAC InChI key

PQGCEDQWHSBAJP-TXICZTDVSA-N
PRP

wwPDB Information

Atom count

35 (22 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide

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



PRP : Atoms of Molecule

Total Number of Atoms: 35
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 1.414 -0.754 0.218
2 C2 C C2 R N N 0 2.82 -0.609 -0.404
3 C3 C C3 S N N 0 2.562 0.095 -1.754
4 C4 C C4 R N N 0 1.03 0.291 -1.792
5 C5 C C5 N N N 0 0.494 0.087 -3.21
6 O1 O O1 N N N 0 1.147 0.334 1.104
7 O2 O O2 N N N 0 3.658 0.195 0.428
8 O3 O O3 N N N 0 3.23 1.357 -1.796
9 O4 O O4 N N N 0 0.508 -0.725 -0.905
10 O5 O O5 N N N 0 -0.929 0.203 -3.202
11 P P P N N N 0 -1.423 -0.021 -4.718
12 O1P O O1P N N N 0 -1.007 -1.364 -5.179
13 O2P O O2P N N N 0 -3.027 0.096 -4.784
14 O3P O O3P N N N 0 -0.764 1.099 -5.668
15 PA P PA R N N 0 0.157 -0.225 2.244
16 O1A O O1A N N N 0 -1.092 -0.711 1.617
17 O2A O O2A N N N 0 0.871 -1.437 3.027
18 O3A O O3A N N N 0 -0.186 0.955 3.283
19 PB P PB N N N 0 -1.175 0.329 4.389
20 O1B O O1B N N N 0 -0.498 -0.793 5.075
21 O2B O O2B N N N 0 -1.562 1.461 5.465
22 O3B O O3B N N N 0 -2.512 -0.208 3.671
23 H1 H H1 N N N 0 1.33 -1.703 0.748
24 H2 H H2 N N N 0 3.27 -1.589 -0.564
25 H3 H H3 N N N 0 2.886 -0.535 -2.582
26 H4 H H4 N N N 0 0.767 1.284 -1.426
27 H51 H H51 N N N 0 0.916 0.845 -3.87
28 H52 H H52 N N N 0 0.776 -0.902 -3.566
29 HO2 H HO2 N N Y 0 3.785 -0.292 1.253
30 HO3 H HO3 N N Y 0 4.177 1.174 -1.74
31 HOP2 H HOP2 N N N 0 -3.28 -0.044 -5.706
32 HOP3 H HOP3 N N N 0 -1.059 1.957 -5.335
33 HOA2 H HOA2 N N N 0 1.679 -1.079 3.42
34 HOB2 H HOB2 N N N 0 -2.153 1.046 6.108
35 HOB3 H HOB3 N N N 0 -2.921 0.552 3.236



PRP : Chemical Bonds

Total Number of Bonds: 35
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.54 N N
2 C1 O1 C O sing 1.43 N N
3 C1 O4 C O sing 1.44 N N
4 C1 H1 C H sing 1.09 N N
5 C2 C3 C C sing 1.54 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 1.54 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 1.45 N N
13 C4 H4 C H sing 1.09 N N
14 C5 O5 C O sing 1.43 N N
15 C5 H51 C H sing 1.09 N N
16 C5 H52 C H sing 1.09 N N
17 O1 PA O P sing 1.61 N N
18 O2 HO2 O H sing 0.97 N N
19 O3 HO3 O H sing 0.97 N N
20 O5 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
26 PA O1A P O doub 1.48 N N
27 PA O2A P O sing 1.61 N N
28 PA O3A P O sing 1.61 N N
29 O2A HOA2 O H sing 0.97 N N
30 O3A PB O P sing 1.61 N N
31 PB O1B P O doub 1.48 N N
32 PB O2B P O sing 1.61 N N
33 PB O3B P O sing 1.61 N N
34 O2B HOB2 O H sing 0.97 N N
35 O3B HOB3 O H sing 0.97 N N



PRP : Used in PDB Entries

Total Number of PDB Entries: 87
Ligand Code PDB Entry ID Type Total Distinct
PRP 1d6n Open in New Window Bound ligand 2 1
PRP 1fsg Open in New Window Bound ligand 2 1
PRP 1i0i Open in New Window Bound ligand 2 1
PRP 1i0l Open in New Window Bound ligand 2 1
PRP 1i13 Open in New Window Bound ligand 2 1
PRP 1i14 Open in New Window Bound ligand 2 1
PRP 1jls Open in New Window Bound ligand 1 1
PRP 1kgz Open in New Window Bound ligand 2 1
PRP 1l1r Open in New Window Bound ligand 1 1
PRP 1lh0 Open in New Window Bound ligand 1 1
PRP 1opr Open in New Window Bound ligand 1 1
PRP 1p18 Open in New Window Bound ligand 2 1
PRP 1tc2 Open in New Window Bound ligand 2 1
PRP 1vst Open in New Window Bound ligand 1 1
PRP 1z7n Open in New Window Bound ligand 4 1
PRP 1zn7 Open in New Window Bound ligand 2 1
PRP 1zvw Open in New Window Bound ligand 1 1
PRP 1zxy Open in New Window Bound ligand 4 1
PRP 1zyk Open in New Window Bound ligand 4 1
PRP 2e5c Open in New Window Bound ligand 2 1
PRP 2ps1 Open in New Window Bound ligand 2 1
PRP 3c2f Open in New Window Bound ligand 1 1
PRP 3c2v Open in New Window Bound ligand 1 1
PRP 3dkj Open in New Window Bound ligand 2 1
PRP 3dkl Open in New Window Bound ligand 2 1
PRP 3g6w Open in New Window Bound ligand 2 1
PRP 3gbr Open in New Window Bound ligand 2 1
PRP 3qqs Open in New Window Bound ligand 3 1
PRP 3qs8 Open in New Window Bound ligand 4 1
PRP 3qsa Open in New Window Bound ligand 2 1
PRP 3r6c Open in New Window Bound ligand 2 1
PRP 3r88 Open in New Window Bound ligand 2 1
PRP 3twp Open in New Window Bound ligand 4 1
PRP 3uu1 Open in New Window Bound ligand 4 1
PRP 4giu Open in New Window Bound ligand 2 1
PRP 4gkm Open in New Window Bound ligand 2 1
PRP 4n5v Open in New Window Bound ligand 2 1
PRP 4n93 Open in New Window Bound ligand 2 1
PRP 4owm Open in New Window Bound ligand 2 1
PRP 4own Open in New Window Bound ligand 1 1
PRP 4owo Open in New Window Bound ligand 2 1
PRP 4owq Open in New Window Bound ligand 2 1
PRP 4owu Open in New Window Bound ligand 2 1
PRP 4rv4 Open in New Window Bound ligand 3 1
PRP 4x58 Open in New Window Bound ligand 1 1
PRP 4x59 Open in New Window Bound ligand 2 1
PRP 4x5b Open in New Window Bound ligand 2 1
PRP 4x5c Open in New Window Bound ligand 1 1
PRP 4z1o Open in New Window Bound ligand 2 1
PRP 4zof Open in New Window Bound ligand 2 1
PRP 4zoj Open in New Window Bound ligand 2 1
PRP 4zok Open in New Window Bound ligand 2 1
PRP 5byt Open in New Window Bound ligand 2 1
PRP 5c7s Open in New Window Bound ligand 2 1
PRP 5hkf Open in New Window Bound ligand 2 1
PRP 5ubi Open in New Window Bound ligand 2 1
PRP 5y07 Open in New Window Bound ligand 2 1
PRP 6ck5 Open in New Window Bound ligand 2 1
PRP 6d9r Open in New Window Bound ligand 2 1
PRP 6dlq Open in New Window Bound ligand 1 1
PRP 6dlr Open in New Window Bound ligand 1 1
PRP 6dls Open in New Window Bound ligand 1 1
PRP 6dlt Open in New Window Bound ligand 1 1
PRP 6fca Open in New Window Bound ligand 1 1
PRP 6fch Open in New Window Bound ligand 2 1
PRP 6fci Open in New Window Bound ligand 4 1
PRP 6fct Open in New Window Bound ligand 1 1
PRP 6fcy Open in New Window Bound ligand 1 1
PRP 6fd4 Open in New Window Bound ligand 2 1
PRP 6fd5 Open in New Window Bound ligand 1 1
PRP 6ftt Open in New Window Bound ligand 4 1
PRP 6fu2 Open in New Window Bound ligand 2 1
PRP 6fua Open in New Window Bound ligand 2 1
PRP 6hgq Open in New Window Bound ligand 4 1
PRP 6r02 Open in New Window Bound ligand 4 1
PRP 6ta0 Open in New Window Bound ligand 2 1
PRP 6yqq Open in New Window Bound ligand 1 1
PRP 7dah Open in New Window Bound ligand 2 1
PRP 7dsj Open in New Window Bound ligand 2 1
PRP 7p0h Open in New Window Bound ligand 4 1
PRP 7z6r Open in New Window Bound ligand 2 1
PRP 7z8u Open in New Window Bound ligand 1 1
PRP 8ap0 Open in New Window Bound ligand 1 1
PRP 8dbk Open in New Window Bound ligand 1 1
PRP 8dbl Open in New Window Bound ligand 6 1
PRP 8dbm Open in New Window Bound ligand 12 1
PRP 8j8j Open in New Window Bound ligand 3 1