Chemical Components in the PDB

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VQB : Summary

Code

VQB

One-letter code

X

Molecule name

4-chloro-6-(pyrrolidin-1-yl)pyrimidin-5-amine

Systematic names

ProgramVersionName
ACDLabs 12.01 4-chloro-6-(pyrrolidin-1-yl)pyrimidin-5-amine
OpenEye OEToolkits 2.0.7 4-chloranyl-6-pyrrolidin-1-yl-pyrimidin-5-amine

Formula

C8 H11 Cl N4

Formal charge

0

Molecular weight

198.653 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Nc1c(ncnc1Cl)N1CCCC1
SMILES CACTVS 3.385 Nc1c(Cl)ncnc1N2CCCC2
SMILES OpenEye OEToolkits 2.0.7 c1nc(c(c(n1)Cl)N)N2CCCC2
Canonical SMILES CACTVS 3.385 Nc1c(Cl)ncnc1N2CCCC2
Canonical SMILES OpenEye OEToolkits 2.0.7 c1nc(c(c(n1)Cl)N)N2CCCC2

IUPAC InChI

InChI=1S/C8H11ClN4/c9-7-6(10)8(12-5-11-7)13-3-1-2-4-13/h5H,1-4,10H2

IUPAC InChI key

HGBSHFZMWYKLPY-UHFFFAOYSA-N
VQB

wwPDB Information

Atom count

24 (13 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-09-02

Last modified at

2022-10-28

Status

Released

Obsoleted

Not Assigned



VQB : Atoms of Molecule

Total Number of Atoms: 24
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 1.952 -1.513 -0.261
2 C7 C C1 N N N 0 -2.718 -0.798 0.609
3 N2 N N2 N N N 0 0.684 1.808 0.46
4 C1 C C2 N Y N 0 -0.42 -0.36 0.303
5 C5 C C3 N N N 0 -3.538 1.174 -0.536
6 C6 C C4 N N N 0 -3.787 -0.353 -0.412
7 N3 N N3 N N N 0 -1.649 0.217 0.592
8 C4 C C5 N N N 0 -1.996 1.251 -0.406
9 C3 C C6 N Y N 0 1.941 -0.202 -0.056
10 C2 C C7 N Y N 0 0.739 0.426 0.237
11 CL CL CL1 N N N 0 3.412 0.715 -0.152
12 C C C8 N Y N 0 0.843 -2.22 -0.19
13 N N N4 N Y N 0 -0.322 -1.667 0.084
14 H1 H H1 N N N 0 -3.158 -0.856 1.604
15 H2 H H2 N N N 0 -2.313 -1.768 0.322
16 H3 H H3 N N N 0 1.494 2.34 0.41
17 H4 H H4 N N N 0 -0.164 2.233 0.663
18 H5 H H5 N N N 0 -3.867 1.546 -1.506
19 H6 H H6 N N N 0 -4.026 1.716 0.274
20 H7 H H7 N N N 0 -3.632 -0.847 -1.372
21 H8 H H8 N N N 0 -4.789 -0.55 -0.032
22 H9 H H9 N N N 0 -1.523 1.029 -1.363
23 H10 H H10 N N N 0 -1.694 2.237 -0.053
24 H11 H H11 N N N 0 0.889 -3.285 -0.363



VQB : Chemical Bonds

Total Number of Bonds: 25
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C N C doub 1.32 N Y
2 N1 C3 N C sing 1.33 N Y
3 C N C N sing 1.32 N Y
4 C3 CL C CL sing 1.74 N N
5 C3 C2 C C doub 1.39 N Y
6 N C1 N C doub 1.33 N Y
7 C2 C1 C C sing 1.4 N Y
8 C2 N2 C N sing 1.4 N N
9 C1 N3 C N sing 1.39 N N
10 C7 N3 C N sing 1.47 N N
11 C7 C6 C C sing 1.54 N N
12 C4 C5 C C sing 1.55 N N
13 C4 N3 C N sing 1.48 N N
14 C5 C6 C C sing 1.55 N N
15 C7 H1 C H sing 1.09 N N
16 C7 H2 C H sing 1.09 N N
17 N2 H3 N H sing 0.97 N N
18 N2 H4 N H sing 0.97 N N
19 C5 H5 C H sing 1.09 N N
20 C5 H6 C H sing 1.09 N N
21 C6 H7 C H sing 1.09 N N
22 C6 H8 C H sing 1.09 N N
23 C4 H9 C H sing 1.09 N N
24 C4 H10 C H sing 1.09 N N
25 C H11 C H sing 1.08 N N



VQB : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
VQB 7fks Open in New Window Bound ligand 1 1