Chemical Components in the PDB

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C2M : Summary

Code

C2M

One-letter code

X

Molecule name

5-(3,4-DICHLOROPHENYL)-6-METHYLPYRIMIDINE-2,4-DIAMINE

Synonyms

METOPRINE
METHODICHLOROPHEN

Systematic names

ProgramVersionName
ACDLabs 10.04 5-(3,4-dichlorophenyl)-6-methylpyrimidine-2,4-diamine
OpenEye OEToolkits 1.5.0 5-(3,4-dichlorophenyl)-6-methyl-pyrimidine-2,4-diamine

Formula

C11 H10 Cl2 N4

Formal charge

0

Molecular weight

269.13 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 Clc2ccc(c1c(nc(nc1C)N)N)cc2Cl
SMILES CACTVS 3.341 Cc1nc(N)nc(N)c1c2ccc(Cl)c(Cl)c2
SMILES OpenEye OEToolkits 1.5.0 Cc1c(c(nc(n1)N)N)c2ccc(c(c2)Cl)Cl
Canonical SMILES CACTVS 3.341 Cc1nc(N)nc(N)c1c2ccc(Cl)c(Cl)c2
Canonical SMILES OpenEye OEToolkits 1.5.0 Cc1c(c(nc(n1)N)N)c2ccc(c(c2)Cl)Cl

IUPAC InChI

InChI=1S/C11H10Cl2N4/c1-5-9(10(14)17-11(15)16-5)6-2-3-7(12)8(13)4-6/h2-4H,1H3,(H4,14,15,16,17)

IUPAC InChI key

VQJHOPSWBGJHQS-UHFFFAOYSA-N
C2M

wwPDB Information

Atom count

27 (17 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAD

Is modified

No

Standard parent

Not Assigned

Defined at

2005-09-01

Last modified at

2020-05-27

Status

Released

Obsoleted

Not Assigned



C2M : 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 N1 N N1 N Y N 0 3.511 1.068 0.601
2 C2 C C2 N Y N 0 4.224 0.172 -0.067
3 N2 N N2 N Y N 0 3.661 -0.869 -0.662
4 C3 C C3 N Y N 0 2.347 -1.053 -0.61
5 C4 C C4 N Y N 0 1.558 -0.124 0.096
6 C5 C C5 N Y N 0 2.196 0.957 0.701
7 C6 C C6 N Y N 0 0.087 -0.286 0.183
8 C7 C C7 N Y N 0 -0.756 0.657 -0.403
9 C8 C C8 N Y N 0 -2.126 0.498 -0.324
10 C9 C C9 N Y N 0 -2.661 -0.59 0.346
11 C10 C C10 N Y N 0 -1.827 -1.525 0.934
12 C11 C C11 N Y N 0 -0.457 -1.379 0.856
13 N3 N N3 N N N 0 5.596 0.329 -0.144
14 N4 N N4 N N N 0 1.763 -2.141 -1.232
15 C12 C C12 N N N 0 1.399 1.983 1.463
16 CL1 CL CL1 N N N 0 -4.384 -0.78 0.449
17 CL2 CL CL2 N N N 0 -3.178 1.667 -1.058
18 H7 H H7 N N N 0 -0.339 1.505 -0.925
19 H10 H H10 N N N 0 -2.25 -2.372 1.455
20 H11 H H11 N N N 0 0.192 -2.11 1.315
21 HN31 H 1HN3 N N N 0 6.023 1.086 0.287
22 HN32 H 2HN3 N N N 0 6.132 -0.318 -0.629
23 HN41 H 1HN4 N N N 0 2.315 -2.779 -1.713
24 HN42 H 2HN4 N N N 0 0.803 -2.267 -1.189
25 H121 H 1H12 N N N 0 1.095 2.783 0.788
26 H122 H 2H12 N N N 0 0.513 1.512 1.89
27 H123 H 3H12 N N N 0 2.011 2.397 2.264



C2M : Chemical Bonds

Total Number of Bonds: 28
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C doub 1.33 N Y
2 N1 C5 N C sing 1.32 N Y
3 C2 N2 C N sing 1.32 N Y
4 C2 N3 C N sing 1.38 N N
5 N2 C3 N C doub 1.33 N Y
6 C3 C4 C C sing 1.41 N Y
7 C3 N4 C N sing 1.38 N N
8 C4 C5 C C doub 1.39 N Y
9 C4 C6 C C sing 1.48 N Y
10 C5 C12 C C sing 1.51 N N
11 C6 C7 C C doub 1.39 N Y
12 C6 C11 C C sing 1.39 N Y
13 C7 C8 C C sing 1.38 N Y
14 C7 H7 C H sing 1.08 N N
15 C8 C9 C C doub 1.39 N Y
16 C8 CL2 C CL sing 1.74 N N
17 C9 C10 C C sing 1.38 N Y
18 C9 CL1 C CL sing 1.74 N N
19 C10 C11 C C doub 1.38 N Y
20 C10 H10 C H sing 1.08 N N
21 C11 H11 C H sing 1.08 N N
22 N3 HN31 N H sing 0.97 N N
23 N3 HN32 N H sing 0.97 N N
24 N4 HN41 N H sing 0.97 N N
25 N4 HN42 N H sing 0.97 N N
26 C12 H121 C H sing 1.09 N N
27 C12 H122 C H sing 1.09 N N
28 C12 H123 C H sing 1.09 N N



C2M : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
C2M 2aov Open in New Window Bound ligand 2 1