Chemical Components in the PDB

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ORP : Summary

Code

ORP

One-letter code

X

Molecule name

2-DEOXY-5-PHOSPHONO-RIBOSE

Systematic names

ProgramVersionName
ACDLabs 10.04 2-deoxy-5-O-phosphono-alpha-D-erythro-pentofuranose
OpenEye OEToolkits 1.5.0 [(2R,3S,5S)-3,5-dihydroxyoxolan-2-yl]methyl dihydrogen phosphate

Formula

C5 H11 O7 P

Formal charge

0

Molecular weight

214.11 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(OCC1OC(O)CC1O)(O)O
SMILES CACTVS 3.341 O[CH]1C[CH](O)[CH](CO[P](O)(O)=O)O1
SMILES OpenEye OEToolkits 1.5.0 C1C(C(OC1O)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.341 O[C@@H]1C[C@H](O)[C@@H](CO[P](O)(O)=O)O1
Canonical SMILES OpenEye OEToolkits 1.5.0 C1[C@@H]([C@H](O[C@@H]1O)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C5H11O7P/c6-3-1-5(7)12-4(3)2-11-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5-/m0/s1

IUPAC InChI key

KKZFLSZAWCYPOC-LMVFSUKVSA-N
ORP

wwPDB Information

Atom count

24 (13 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



ORP : Atoms of Molecule

Total Number of Atoms: 24
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 1.067 -0.392 -2.79
2 O1 O O1 N N N 0 2.032 0.149 -3.694
3 C2 C C2 N N N 0 -0.345 -0.352 -3.424
4 C3 C C3 S N N 0 -1.238 -0.338 -2.153
5 O3 O O3 N N N 0 -2.484 0.31 -2.414
6 C4 C C4 R N N 0 -0.384 0.479 -1.161
7 O4 O O4 N N N 0 0.975 0.424 -1.611
8 C5 C C5 N N N 0 -0.492 -0.127 0.238
9 O5 O O5 N N N 0 0.3 0.635 1.15
10 P P P N N N 0 0.14 -0.055 2.596
11 O1P O O1P N N N 0 0.617 -1.454 2.529
12 O2P O O2P N N N 0 1.012 0.757 3.678
13 O3P O O3P N N Y 0 -1.408 -0.035 3.032
14 H1 H H1 N N N 0 1.333 -1.414 -2.522
15 HO1 H HO1 N N N 0 2.886 0.12 -3.241
16 H21 H 1H2 N N N 0 -0.486 0.554 -4.013
17 H22 H 2H2 N N N 0 -0.531 -1.241 -4.026
18 H3 H H3 N N N 0 -1.4 -1.351 -1.783
19 HO3 H HO3 N N N 0 -2.927 -0.201 -3.104
20 H4 H H4 N N N 0 -0.727 1.513 -1.143
21 H51 H 1H5 N N N 0 -1.533 -0.112 0.562
22 H52 H 2H5 N N N 0 -0.133 -1.156 0.217
23 HOP2 H 2HOP N N N 0 0.889 0.312 4.528
24 HOP3 H 3HOP N N N 0 -1.678 0.892 3.063



ORP : Chemical Bonds

Total Number of Bonds: 24
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 O1 C O sing 1.43 N N
2 C1 C2 C C sing 1.55 N N
3 C1 O4 C O sing 1.44 N N
4 C1 H1 C H sing 1.09 N N
5 O1 HO1 O H sing 0.97 N N
6 C2 C3 C C sing 1.55 N N
7 C2 H21 C H sing 1.09 N N
8 C2 H22 C H sing 1.09 N N
9 C3 O3 C O sing 1.43 N N
10 C3 C4 C C sing 1.54 N N
11 C3 H3 C H sing 1.09 N N
12 O3 HO3 O H sing 0.97 N N
13 C4 O4 C O sing 1.43 N N
14 C4 C5 C C sing 1.53 N N
15 C4 H4 C H sing 1.09 N N
16 C5 O5 C O sing 1.43 N N
17 C5 H51 C H sing 1.09 N N
18 C5 H52 C H sing 1.09 N N
19 O5 P O P sing 1.61 N N
20 P O1P P O doub 1.48 N N
21 P O2P P O sing 1.61 N N
22 P O3P P O sing 1.61 N N
23 O2P HOP2 O H sing 0.97 N N
24 O3P HOP3 O H sing 0.97 N N



ORP : Used in PDB Entries

Total Number of PDB Entries: 41
Ligand Code PDB Entry ID Type Total Distinct
ORP 1g5d Open in New Window Polymer component 1 1
ORP 1giz Open in New Window Polymer component 1 1
ORP 1sjk Open in New Window Polymer component 1 1
ORP 1ssp Open in New Window Polymer component 1 1
ORP 2ddg Open in New Window Polymer component 1 1
ORP 2dem Open in New Window Polymer component 1 1
ORP 2dp6 Open in New Window Polymer component 1 1
ORP 2hsk Open in New Window Polymer component 1 1
ORP 2hsl Open in New Window Polymer component 1 1
ORP 2m3p Open in New Window Polymer component 1 1
ORP 2m43 Open in New Window Polymer component 1 1
ORP 2o7w Open in New Window Polymer component 1 1
ORP 2o7y Open in New Window Polymer component 1 1
ORP 2o80 Open in New Window Polymer component 1 1
ORP 3waz Open in New Window Polymer component 2 1
ORP 4jgc Open in New Window Polymer component 1 1
ORP 4skn Open in New Window Polymer component 1 1
ORP 4xeg Open in New Window Polymer component 1 1
ORP 4yig Open in New Window Polymer component 3 1
ORP 4z3a Open in New Window Polymer component 1 1
ORP 4z47 Open in New Window Polymer component 1 1
ORP 4z7b Open in New Window Polymer component 1 1
ORP 4z7z Open in New Window Polymer component 1 1
ORP 5cl4 Open in New Window Polymer component 0 1
ORP 5cl5 Open in New Window Polymer component 0 1
ORP 5cl6 Open in New Window Polymer component 0 1
ORP 5cl7 Open in New Window Polymer component 0 1
ORP 5cl8 Open in New Window Polymer component 1 1
ORP 5cl9 Open in New Window Polymer component 1 1
ORP 5cla Open in New Window Polymer component 1 1
ORP 5cys Open in New Window Polymer component 1 1
ORP 5uuf Open in New Window Polymer component 1 1
ORP 5uug Open in New Window Polymer component 1 1
ORP 6ajo Open in New Window Polymer component 1 1
ORP 6iod Open in New Window Polymer component 2 1
ORP 6l6s Open in New Window Polymer component 2 1
ORP 6vjw Open in New Window Polymer component 1 1
ORP 7kz1 Open in New Window Polymer component 1 1
ORP 7lxh Open in New Window Polymer component 1 1
ORP 7lxj Open in New Window Polymer component 1 1
ORP 8dwd Open in New Window Polymer component 1 1