Chemical Components in the PDB

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AHD : Summary

Code

AHD

One-letter code

X

Molecule name

4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE

Synonyms

ALENDRONATE
FOSAMAX (TM)

Systematic names

ProgramVersionName
ACDLabs 12.01 (4-amino-1-hydroxybutane-1,1-diyl)bis(phosphonate)
OpenEye OEToolkits 1.7.2 4-azanyl-1,1-diphosphonato-butan-1-ol

Formula

C4 H9 N O7 P2

Formal charge

-4

Molecular weight

245.064 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 [O-]P([O-])(=O)C(O)(CCCN)P(=O)([O-])[O-]
SMILES CACTVS 3.370 NCCCC(O)([P]([O-])([O-])=O)[P]([O-])([O-])=O
SMILES OpenEye OEToolkits 1.7.2 C(CC(O)(P(=O)([O-])[O-])P(=O)([O-])[O-])CN
Canonical SMILES CACTVS 3.370 NCCCC(O)([P]([O-])([O-])=O)[P]([O-])([O-])=O
Canonical SMILES OpenEye OEToolkits 1.7.2 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)/p-4

IUPAC InChI key

OGSPWJRAVKPPFI-UHFFFAOYSA-J
AHD

wwPDB Information

Atom count

23 (14 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2005-01-11

Last modified at

2020-05-26

Status

Released

Obsoleted

Not Assigned



AHD : Atoms of Molecule

Total Number of Atoms: 23
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C2 N N N 0 2.296 -0.478 -0.227
2 C3 C C3 N N N 0 3.429 -1.271 0.428
3 C7 C C7 N N N 0 0.949 -1.04 0.232
4 C8 C C8 N N N 0 -0.184 -0.247 -0.422
5 O12 O O12 N N N -1 -1.95 -2.383 -0.404
6 P9 P P9 N N N 0 -1.789 -0.917 0.124
7 O10 O O10 N N N -1 -2.947 -0.027 -0.443
8 O11 O O11 N N N 0 -1.849 -0.917 1.69
9 P14 P P14 N N N 0 -0.059 1.505 0.065
10 O15 O O15 N N N -1 -0.171 1.624 1.623
11 O16 O O16 N N N -1 -1.219 2.317 -0.605
12 O17 O O17 N N N 0 1.32 2.081 -0.405
13 O13 O O13 N N N 0 -0.082 -0.355 -1.844
14 N4 N N4 N N N 0 4.723 -0.731 -0.013
15 H21 H 1H2 N N N 0 2.371 0.57 0.064
16 H22 H 2H2 N N N 0 2.374 -0.56 -1.311
17 H31 H 1H3 N N N 0 3.355 -2.318 0.136
18 H32 H 2H3 N N N 0 3.352 -1.188 1.512
19 H71 H 1H7 N N N 0 0.875 -2.088 -0.059
20 H72 H 2H7 N N N 0 0.872 -0.958 1.316
21 H13 H H13 N N N 0 -0.152 -1.295 -2.058
22 HN41 H 1HN4 N N N 0 4.792 0.202 0.365
23 HN42 H 2HN4 N N N 0 5.436 -1.281 0.441



AHD : Chemical Bonds

Total Number of Bonds: 22
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C2 C3 C C sing 1.53 N N
2 C2 C7 C C sing 1.53 N N
3 C2 H21 C H sing 1.09 N N
4 C2 H22 C H sing 1.09 N N
5 C3 N4 C N sing 1.47 N N
6 C3 H31 C H sing 1.09 N N
7 C3 H32 C H sing 1.09 N N
8 C7 C8 C C sing 1.53 N N
9 C7 H71 C H sing 1.09 N N
10 C7 H72 C H sing 1.09 N N
11 C8 P9 C P sing 1.82 N N
12 C8 P14 C P sing 1.82 N N
13 C8 O13 C O sing 1.43 N N
14 O12 P9 O P sing 1.57 N N
15 P9 O10 P O sing 1.57 N N
16 P9 O11 P O doub 1.57 N N
17 P14 O15 P O sing 1.57 N N
18 P14 O16 P O sing 1.57 N N
19 P14 O17 P O doub 1.57 N N
20 O13 H13 O H sing 0.97 N N
21 N4 HN41 N H sing 1.01 N N
22 N4 HN42 N H sing 1.01 N N



AHD : Used in PDB Entries

Total Number of PDB Entries: 9
Ligand Code PDB Entry ID Type Total Distinct
AHD 1yhm Open in New Window Bound ligand 3 1
AHD 2f92 Open in New Window Bound ligand 1 1
AHD 3sdt Open in New Window Bound ligand 1 1
AHD 4kqu Open in New Window Bound ligand 1 1
AHD 6ggj Open in New Window Bound ligand 2 1
AHD 7ao0 Open in New Window Bound ligand 2 1
AHD 7ao1 Open in New Window Bound ligand 2 1
AHD 7ao2 Open in New Window Bound ligand 2 1
AHD 7ao3 Open in New Window Bound ligand 2 1