Chemical Components in the PDB

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1QO : Summary

Code

1QO

One-letter code

X

Molecule name

N-benzyl-4-(pyridin-3-yl)pyrimidin-2-amine

Systematic names

ProgramVersionName
ACDLabs 12.01 N-benzyl-4-(pyridin-3-yl)pyrimidin-2-amine
OpenEye OEToolkits 1.7.6 N-(phenylmethyl)-4-pyridin-3-yl-pyrimidin-2-amine

Formula

C16 H14 N4

Formal charge

0

Molecular weight

262.309 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 n1c(ccnc1NCc2ccccc2)c3cccnc3
SMILES CACTVS 3.370 C(Nc1nccc(n1)c2cccnc2)c3ccccc3
SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)CNc2nccc(n2)c3cccnc3
Canonical SMILES CACTVS 3.370 C(Nc1nccc(n1)c2cccnc2)c3ccccc3
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)CNc2nccc(n2)c3cccnc3

IUPAC InChI

InChI=1S/C16H14N4/c1-2-5-13(6-3-1)11-19-16-18-10-8-15(20-16)14-7-4-9-17-12-14/h1-10,12H,11H2,(H,18,19,20)

IUPAC InChI key

JTYLHRZXSYVYMO-UHFFFAOYSA-N
1QO

wwPDB Information

Atom count

34 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-04-27

Last modified at

2013-09-13

Status

Released

Obsoleted

Not Assigned



1QO : Atoms of Molecule

Total Number of Atoms: 34
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -1.373 -0.239 -0.0040
2 C2 C C2 N Y N 0 -0.125 -0.837 0.0090
3 N3 N N3 N Y N 0 0.956 -0.074 0.0
4 C4 C C4 N Y N 0 2.288 -2.011 0.033
5 N4 N N4 N Y N 0 5.725 0.432 -0.1
6 C5 C C5 N Y N 0 2.17 -0.619 0.011
7 C6 C C6 N Y N 0 3.38 0.239 0.0010
8 C11 C C11 N Y N 0 -3.799 -0.177 -0.0040
9 C12 C C12 N Y N 0 -4.358 0.217 -1.206
10 C13 C C13 N Y N 0 -5.474 1.033 -1.215
11 C1 C C1 N N N 0 -2.582 -1.066 0.0060
12 N2 N N2 N Y N 0 -0.044 -2.16 0.034
13 C3 C C3 N Y N 0 1.131 -2.77 0.047
14 C7 C C7 N Y N 0 3.266 1.629 0.085
15 C8 C C8 N Y N 0 4.426 2.385 0.072
16 C9 C C9 N Y N 0 5.649 1.746 -0.023
17 C10 C C10 N Y N 0 4.65 -0.329 -0.092
18 C14 C C14 N Y N 0 -6.032 1.454 -0.022
19 C15 C C15 N Y N 0 -5.473 1.059 1.179
20 C16 C C16 N Y N 0 -4.354 0.249 1.188
21 H3 H H3 N N N 0 -1.447 0.728 -0.014
22 H5 H H5 N N N 0 3.259 -2.484 0.043
23 H10 H H10 N N N 0 -3.921 -0.112 -2.138
24 H11 H H11 N N N 0 -5.91 1.341 -2.154
25 H2 H H2 N N N 0 -2.592 -1.705 -0.877
26 H1 H H1 N N N 0 -2.592 -1.685 0.903
27 H4 H H4 N N N 0 1.186 -3.848 0.068
28 H6 H H6 N N N 0 2.298 2.102 0.158
29 H7 H H7 N N N 0 4.376 3.462 0.135
30 H8 H H8 N N N 0 6.555 2.333 -0.033
31 H9 H H9 N N N 0 4.753 -1.402 -0.158
32 H12 H H12 N N N 0 -6.904 2.091 -0.029
33 H13 H H13 N N N 0 -5.909 1.389 2.111
34 H14 H H14 N N N 0 -3.918 -0.06 2.127



1QO : Chemical Bonds

Total Number of Bonds: 36
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C3 N2 C N doub 1.32 N Y
2 C3 C4 C C sing 1.38 N Y
3 N2 C2 N C sing 1.33 N Y
4 C4 C5 C C doub 1.4 N Y
5 C2 N1 C N sing 1.38 N N
6 C2 N3 C N doub 1.32 N Y
7 N1 C1 N C sing 1.46 N N
8 C5 N3 C N sing 1.33 N Y
9 C5 C6 C C sing 1.48 N N
10 C16 C15 C C doub 1.38 N Y
11 C16 C11 C C sing 1.38 N Y
12 C1 C11 C C sing 1.51 N N
13 C15 C14 C C sing 1.38 N Y
14 C7 C6 C C doub 1.4 N Y
15 C7 C8 C C sing 1.38 N Y
16 C6 C10 C C sing 1.39 N Y
17 C11 C12 C C doub 1.38 N Y
18 C8 C9 C C doub 1.38 N Y
19 C10 N4 C N doub 1.32 N Y
20 C14 C13 C C doub 1.38 N Y
21 C12 C13 C C sing 1.38 N Y
22 C9 N4 C N sing 1.32 N Y
23 N1 H3 N H sing 0.97 N N
24 C4 H5 C H sing 1.08 N N
25 C12 H10 C H sing 1.08 N N
26 C13 H11 C H sing 1.08 N N
27 C1 H2 C H sing 1.09 N N
28 C1 H1 C H sing 1.09 N N
29 C3 H4 C H sing 1.08 N N
30 C7 H6 C H sing 1.08 N N
31 C8 H7 C H sing 1.08 N N
32 C9 H8 C H sing 1.08 N N
33 C10 H9 C H sing 1.08 N N
34 C14 H12 C H sing 1.08 N N
35 C15 H13 C H sing 1.08 N N
36 C16 H14 C H sing 1.08 N N



1QO : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
1QO 4kb8 Open in New Window Bound ligand 2 1