Chemical Components in the PDB

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ZOL : Summary

Code

ZOL

One-letter code

X

Molecule name

ZOLEDRONIC ACID

Synonyms

(1-HYDROXY-2-IMIDAZOL-1-YLETHYLIDENE)DIPHOSPHONIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 [1-hydroxy-2-(1H-imidazol-1-yl)ethane-1,1-diyl]bis(phosphonic acid)
OpenEye OEToolkits 1.5.0 (1-hydroxy-2-imidazol-1-yl-1-phosphono-ethyl)phosphonic acid

Formula

C5 H10 N2 O7 P2

Formal charge

0

Molecular weight

272.09 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)C(O)(Cn1ccnc1)P(=O)(O)O
SMILES CACTVS 3.341 OC(Cn1ccnc1)([P](O)(O)=O)[P](O)(O)=O
SMILES OpenEye OEToolkits 1.5.0 c1cn(cn1)CC(O)(P(=O)(O)O)P(=O)(O)O
Canonical SMILES CACTVS 3.341 OC(Cn1ccnc1)([P](O)(O)=O)[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cn(cn1)CC(O)(P(=O)(O)O)P(=O)(O)O

IUPAC InChI

InChI=1S/C5H10N2O7P2/c8-5(15(9,10)11,16(12,13)14)3-7-2-1-6-4-7/h1-2,4,8H,3H2,(H2,9,10,11)(H2,12,13,14)

IUPAC InChI key

XRASPMIURGNCCH-UHFFFAOYSA-N
ZOL

wwPDB Information

Atom count

26 (16 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2005-06-06

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



ZOL : Atoms of Molecule

Total Number of Atoms: 26
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O17 O O17 N N N 0 -0.194 -2.838 0.649
2 P14 P P14 N N N 0 -0.602 -1.581 -0.27
3 O16 O O16 N N N 0 0.57 -1.292 -1.335
4 O15 O O15 N N N 0 -1.859 -1.884 -0.99
5 C8 C C8 N N N 0 -0.843 -0.112 0.782
6 P9 P P9 N N N 0 -1.094 1.355 -0.271
7 O10 O O10 N N N 0 -1.307 2.652 0.659
8 O11 O O11 N N N 0 0.198 1.571 -1.206
9 O12 O O12 N N N 0 -2.29 1.154 -1.119
10 O13 O O13 N N N 0 -1.99 -0.304 1.613
11 C7 C C7 N N N 0 0.393 0.095 1.66
12 N15 N N15 N Y N 0 1.579 0.221 0.81
13 C16 C C16 N Y N 0 2.373 -0.786 0.386
14 N17 N N17 N Y N 0 3.325 -0.286 -0.353
15 C18 C C18 N Y N 0 3.18 1.046 -0.42
16 C19 C C19 N Y N 0 2.094 1.383 0.301
17 H17 H H17 N N N 0 0.66 -2.626 1.05
18 H1 H H1 N N N 0 0.665 -2.092 -1.87
19 H10 H H10 N N N 0 -0.507 2.747 1.194
20 H11 H H11 N N N 0 0.024 2.355 -1.745
21 H13 H H13 N N N 0 -2.082 0.493 2.152
22 H71 H 1H7 N N N 0 0.271 1.003 2.251
23 H72 H 2H7 N N N 0 0.513 -0.759 2.326
24 H16 H H16 N N N 0 2.238 -1.833 0.616
25 H18 H H18 N N N 0 3.822 1.728 -0.958
26 H19 H H19 N N N 0 1.704 2.379 0.449



ZOL : 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 O17 P14 O P sing 1.61 N N
2 O17 H17 O H sing 0.97 N N
3 P14 O16 P O sing 1.61 N N
4 P14 O15 P O doub 1.48 N N
5 P14 C8 P C sing 1.82 N N
6 O16 H1 O H sing 0.97 N N
7 C8 P9 C P sing 1.82 N N
8 C8 O13 C O sing 1.43 N N
9 C8 C7 C C sing 1.53 N N
10 P9 O10 P O sing 1.61 N N
11 P9 O11 P O sing 1.61 N N
12 P9 O12 P O doub 1.48 N N
13 O10 H10 O H sing 0.97 N N
14 O11 H11 O H sing 0.97 N N
15 O13 H13 O H sing 0.97 N N
16 C7 N15 C N sing 1.46 N N
17 C7 H71 C H sing 1.09 N N
18 C7 H72 C H sing 1.09 N N
19 N15 C16 N C sing 1.35 N Y
20 N15 C19 N C sing 1.37 N Y
21 C16 N17 C N doub 1.3 N Y
22 C16 H16 C H sing 1.08 N N
23 N17 C18 N C sing 1.34 N Y
24 C18 C19 C C doub 1.35 N Y
25 C18 H18 C H sing 1.08 N N
26 C19 H19 C H sing 1.08 N N



ZOL : Used in PDB Entries

Total Number of PDB Entries: 16
Ligand Code PDB Entry ID Type Total Distinct
ZOL 1zw5 Open in New Window Bound ligand 1 1
ZOL 2e91 Open in New Window Bound ligand 2 1
ZOL 2f8c Open in New Window Bound ligand 1 1
ZOL 2f8z Open in New Window Bound ligand 1 1
ZOL 2f9k Open in New Window Bound ligand 1 1
ZOL 2q58 Open in New Window Bound ligand 2 1
ZOL 3ez3 Open in New Window Bound ligand 4 1
ZOL 3iba Open in New Window Bound ligand 1 1
ZOL 3ldw Open in New Window Bound ligand 4 1
ZOL 3n45 Open in New Window Bound ligand 1 1
ZOL 3n46 Open in New Window Bound ligand 1 1
ZOL 4kfa Open in New Window Bound ligand 1 1
ZOL 4kq5 Open in New Window Bound ligand 1 1
ZOL 4p0v Open in New Window Bound ligand 1 1
ZOL 4p0w Open in New Window Bound ligand 1 1
ZOL 6g31 Open in New Window Bound ligand 12 1