Chemical Components in the PDB

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AZF : Summary

Code

AZF

One-letter code

X

Molecule name

AZAFAGOMINE

Systematic names

ProgramVersionName
ACDLabs 10.04 (3R,4R,5R)-3-(hydroxymethyl)hexahydropyridazine-4,5-diol
OpenEye OEToolkits 1.5.0 (3R,4R,5R)-3-(hydroxymethyl)-1,2-diazinane-4,5-diol

Formula

C5 H12 N2 O3

Formal charge

0

Molecular weight

148.16 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 OC1C(NNCC1O)CO
SMILES CACTVS 3.341 OC[CH]1NNC[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 C1C(C(C(NN1)CO)O)O
Canonical SMILES CACTVS 3.341 OC[C@H]1NNC[C@@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1[C@H]([C@@H]([C@H](NN1)CO)O)O

IUPAC InChI

InChI=1S/C5H12N2O3/c8-2-3-5(10)4(9)1-6-7-3/h3-10H,1-2H2/t3-,4-,5-/m1/s1

IUPAC InChI key

PPPMSBCQTLJPKM-UOWFLXDJSA-N
AZF

wwPDB Information

Atom count

22 (10 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2006-10-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



AZF : Atoms of Molecule

Total Number of Atoms: 22
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O4 O O4 N N N 0 1.035 -2.019 3.505
2 C4 C C4 R N N 0 0.342 -1.618 2.323
3 C3 C C3 R N N 0 1.366 -0.994 1.371
4 O3 O O3 N N N 0 1.769 0.269 1.895
5 C2 C C2 N N N 0 0.756 -0.797 -0.016
6 N N N N N N 0 0.188 -2.044 -0.527
7 C5 C C5 R N N 0 -0.331 -2.836 1.662
8 C6 C C6 N N N 0 -1.475 -3.382 2.52
9 O6 O O6 N N N 0 -2.049 -4.486 1.848
10 N2 N N2 N N N 0 -0.876 -2.476 0.344
11 H4 H H4 N N N 0 1.674 -1.317 3.7
12 HA H HA N N N 0 -0.404 -0.872 2.625
13 H3 H H3 N N N 0 2.265 -1.62 1.311
14 H5 H H5 N N N 0 0.401 -3.649 1.557
15 HB H HB N N N 0 2.289 0.703 1.201
16 H2C1 H 1H2C N N N 0 -0.001 -0.001 0.004
17 H2C2 H 2H2C N N N 0 1.535 -0.445 -0.703
18 H H H N N N 0 -0.202 -1.874 -1.454
19 H2 H H2 N N N 0 -1.322 -3.295 -0.069
20 H6C1 H 1H6C N N N 0 -2.229 -2.61 2.661
21 H6C2 H 2H6C N N N 0 -1.088 -3.705 3.485
22 H6 H H6 N N N 0 -1.352 -4.878 1.294



AZF : 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 O4 C4 O C sing 1.43 N N
2 O4 H4 O H sing 0.97 N N
3 C4 C3 C C sing 1.53 N N
4 C4 C5 C C sing 1.54 N N
5 C4 HA C H sing 1.1 N N
6 C3 O3 C O sing 1.43 N N
7 C3 C2 C C sing 1.53 N N
8 C3 H3 C H sing 1.1 N N
9 O3 HB O H sing 0.97 N N
10 C2 N C N sing 1.46 N N
11 C2 H2C1 C H sing 1.1 N N
12 C2 H2C2 C H sing 1.1 N N
13 N N2 N N sing 1.44 N N
14 N H N H sing 1.02 N N
15 C5 C6 C C sing 1.53 N N
16 C5 N2 C N sing 1.47 N N
17 C5 H5 C H sing 1.1 N N
18 C6 O6 C O sing 1.41 N N
19 C6 H6C1 C H sing 1.09 N N
20 C6 H6C2 C H sing 1.09 N N
21 O6 H6 O H sing 0.97 N N
22 N2 H2 N H sing 1.02 N N



AZF : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
AZF 2j7h Open in New Window Bound ligand 2 1