Chemical Components in the PDB

pdbe.org/chem
spacer

212 : Summary

Code

212

One-letter code

X

Molecule name

ALENDRONATE

Synonyms

(4-AMINO-1-HYDROXY-1-PHOSPHONO-BUTYL)PHOSPHONIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 (4-amino-1-hydroxybutane-1,1-diyl)bis(phosphonic acid)
OpenEye OEToolkits 1.5.0 (4-amino-1-hydroxy-1-phosphono-butyl)phosphonic acid

Formula

C4 H13 N O7 P2

Formal charge

0

Molecular weight

249.096 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)C(O)(CCCN)P(=O)(O)O
SMILES CACTVS 3.341 NCCCC(O)([P](O)(O)=O)[P](O)(O)=O
SMILES OpenEye OEToolkits 1.5.0 C(CC(O)(P(=O)(O)O)P(=O)(O)O)CN
Canonical SMILES CACTVS 3.341 NCCCC(O)([P](O)(O)=O)[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C(CC(O)(P(=O)(O)O)P(=O)(O)O)CN

IUPAC InChI

InChI=1S/C4H13NO7P2/c5-3-1-2-4(6,13(7,8)9)14(10,11)12/h6H,1-3,5H2,(H2,7,8,9)(H2,10,11,12)

IUPAC InChI key

OGSPWJRAVKPPFI-UHFFFAOYSA-N
212

wwPDB Information

Atom count

27 (14 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2006-01-11

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



212 : Atoms of Molecule

Total Number of Atoms: 27
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O2 O O2 N N N 0 1.409 2.059 0.479
2 C7 C C7 N N N 0 -0.178 -0.254 0.407
3 O3 O O3 N N N 0 -0.132 1.687 -1.619
4 C16 C C16 N N N 0 0.94 -1.047 -0.273
5 C19 C C19 N N N 0 2.297 -0.526 0.203
6 O5 O O5 N N N 0 -1.101 2.278 0.636
7 C22 C C22 N N N 0 3.415 -1.319 -0.477
8 P1 P P1 N N N 0 -0.02 1.511 -0.023
9 O9 O O9 N N N 0 -1.899 -0.713 -1.628
10 P8 P P8 N N N 0 -1.796 -0.874 -0.16
11 O10 O O10 N N N 0 -1.936 -2.433 0.219
12 O12 O O12 N N N 0 -2.972 -0.04 0.556
13 O14 O O14 N N N 0 -0.078 -0.41 1.824
14 N25 N N25 N N N 0 4.718 -0.819 -0.02
15 HO2 H HO2 N N N 0 1.452 2.993 0.232
16 HO3 H HO3 N N N 0 0.589 1.172 -2.008
17 H161 H 1H16 N N N 0 0.864 -0.928 -1.354
18 H162 H 2H16 N N N 0 0.845 -2.102 -0.016
19 H191 H 1H19 N N N 0 2.373 -0.645 1.284
20 H192 H 2H19 N N N 0 2.392 0.529 -0.054
21 H221 H 1H22 N N N 0 3.339 -1.2 -1.558
22 H222 H 2H22 N N N 0 3.32 -2.374 -0.221
23 HO10 H HO10 N N N 0 -1.863 -2.494 1.181
24 HO12 H HO12 N N N 0 -3.808 -0.399 0.229
25 HO14 H HO14 N N N 0 -0.167 -1.355 2.008
26 H251 H 1H25 N N N 0 4.786 -1.042 0.961
27 H252 H 2H25 N N N 0 5.421 -1.368 -0.492



212 : Chemical Bonds

Total Number of Bonds: 26
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2 P1 O P sing 1.61 N N
2 O2 HO2 O H sing 0.97 N N
3 C7 C16 C C sing 1.53 N N
4 C7 P1 C P sing 1.82 N N
5 C7 P8 C P sing 1.82 N N
6 C7 O14 C O sing 1.43 N N
7 O3 P1 O P sing 1.61 N N
8 O3 HO3 O H sing 0.97 N N
9 C16 C19 C C sing 1.53 N N
10 C16 H161 C H sing 1.09 N N
11 C16 H162 C H sing 1.09 N N
12 C19 C22 C C sing 1.53 N N
13 C19 H191 C H sing 1.09 N N
14 C19 H192 C H sing 1.09 N N
15 O5 P1 O P doub 1.48 N N
16 C22 N25 C N sing 1.47 N N
17 C22 H221 C H sing 1.09 N N
18 C22 H222 C H sing 1.09 N N
19 O9 P8 O P doub 1.48 N N
20 P8 O10 P O sing 1.61 N N
21 P8 O12 P O sing 1.61 N N
22 O10 HO10 O H sing 0.97 N N
23 O12 HO12 O H sing 0.97 N N
24 O14 HO14 O H sing 0.97 N N
25 N25 H251 N H sing 1.01 N N
26 N25 H252 N H sing 1.01 N N



212 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
212 5dz2 Open in New Window Bound ligand 2 1