Chemical Components in the PDB

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X5M : Summary

Code

X5M

One-letter code

X

Molecule name

(4~{R})-3-[4-(diethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]-4-methyl-4,5-dihydro-1~{H}-pyridazin-6-one

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (4~{R})-3-[4-(diethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]-4-methyl-4,5-dihydro-1~{H}-pyridazin-6-one

Formula

C15 H21 N4 O3

Formal charge

0

Molecular weight

305.352 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CCN(CC)c1ccc(cc1[N](O)=O)C2=NNC(=O)C[CH]2C
SMILES OpenEye OEToolkits 2.0.7 CCN(CC)c1ccc(cc1[N](=O)O)C2=NNC(=O)CC2C
Canonical SMILES CACTVS 3.385 CCN(CC)c1ccc(cc1[N](O)=O)C2=NNC(=O)C[C@H]2C
Canonical SMILES OpenEye OEToolkits 2.0.7 CCN(CC)c1ccc(cc1[N](=O)O)C2=NNC(=O)C[C@H]2C

IUPAC InChI

InChI=1S/C15H21N4O3/c1-4-18(5-2)12-7-6-11(9-13(12)19(21)22)15-10(3)8-14(20)16-17-15/h6-7,9-10H,4-5,8H2,1-3H3,(H,16,20)(H,21,22)/t10-/m1/s1

IUPAC InChI key

OQEBJJKKKZAUSG-SNVBAGLBSA-N
X5M

wwPDB Information

Atom count

42 (22 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-12-01

Last modified at

2021-06-04

Status

Released

Obsoleted

Not Assigned



X5M : Atoms of Molecule

Total Number of Atoms: 42
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C1 N N N 0
2 C02 C C2 N N N 0
3 N03 N N1 N N N 0
4 C04 C C3 N N N 0
5 C05 C C4 N N N 0
6 C06 C C5 N Y N 0
7 C07 C C6 N Y N 0
8 C08 C C7 N Y N 0
9 C09 C C8 N Y N 0
10 C10 C C9 N Y N 0
11 C11 C C10 N Y N 0
12 N12 N N2 N N N 0
13 O13 O O1 N N N 0
14 O14 O O2 N N N 0
15 C15 C C11 N N N 0
16 N16 N N3 N N N 0
17 N17 N N4 N N N 0
18 C18 C C12 N N N 0
19 O19 O O3 N N N 0
20 C20 C C13 N N N 0
21 C21 C C14 R N N 0
22 C22 C C15 N N N 0
23 H1 H H1 N N N 0
24 H2 H H2 N N N 0
25 H3 H H3 N N N 0
26 H4 H H4 N N N 0
27 H5 H H5 N N N 0
28 H6 H H6 N N N 0
29 H7 H H7 N N N 0
30 H8 H H8 N N N 0
31 H9 H H9 N N N 0
32 H10 H H10 N N N 0
33 H15 H H15 N N N 0
34 H11 H H11 N N N 0
35 H12 H H12 N N N 0
36 H13 H H13 N N N 0
37 H16 H H16 N N N 0
38 H17 H H17 N N N 0
39 H18 H H18 N N N 0
40 H19 H H19 N N N 0
41 H20 H H20 N N N 0
42 H14 H H14 N N N 0



X5M : Chemical Bonds

Total Number of Bonds: 43
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C05 C04 C C sing N N
2 C01 C02 C C sing N N
3 C02 N03 C N sing N N
4 C04 N03 C N sing N N
5 N03 C06 N C sing N N
6 O13 N12 O N sing N N
7 C06 C07 C C doub N Y
8 C06 C11 C C sing N Y
9 C07 C08 C C sing N Y
10 N12 C11 N C sing N N
11 N12 O14 N O doub N N
12 C11 C10 C C doub N Y
13 C08 C09 C C doub N Y
14 C10 C09 C C sing N Y
15 C09 C15 C C sing N N
16 C22 C21 C C sing N N
17 C15 C21 C C sing N N
18 C15 N16 C N doub N N
19 C21 C20 C C sing N N
20 N16 N17 N N sing N N
21 C20 C18 C C sing N N
22 N17 C18 N C sing N N
23 C18 O19 C O doub N N
24 C01 H1 C H sing N N
25 C01 H2 C H sing N N
26 C01 H3 C H sing N N
27 C02 H4 C H sing N N
28 C02 H5 C H sing N N
29 C04 H6 C H sing N N
30 C04 H7 C H sing N N
31 C05 H8 C H sing N N
32 C05 H9 C H sing N N
33 C05 H10 C H sing N N
34 C07 H11 C H sing N N
35 C08 H12 C H sing N N
36 C10 H13 C H sing N N
37 C20 H15 C H sing N N
38 C20 H16 C H sing N N
39 C21 H17 C H sing N N
40 C22 H18 C H sing N N
41 C22 H19 C H sing N N
42 C22 H20 C H sing N N
43 N17 H14 N H sing N N



X5M : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
X5M 7eg1 Open in New Window Bound ligand 2 1
X5M 7kwe Open in New Window Bound ligand 4 1
X5M 7lrc Open in New Window Bound ligand 2 1
X5M 7lrd Open in New Window Bound ligand 2 1