Chemical Components in the PDB

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VSY : Summary

Code

VSY

One-letter code

X

Molecule name

(3S)-1-[1-(2-aminopyrimidin-4-yl)-1H-pyrazolo[4,3-c]pyridin-6-yl]-3-methylpent-1-yn-3-ol

Systematic names

ProgramVersionName
ACDLabs 12.01 (3S)-1-[1-(2-aminopyrimidin-4-yl)-1H-pyrazolo[4,3-c]pyridin-6-yl]-3-methylpent-1-yn-3-ol
OpenEye OEToolkits 2.0.7 (3~{S})-1-[1-(2-azanylpyrimidin-4-yl)pyrazolo[4,3-c]pyridin-6-yl]-3-methyl-pent-1-yn-3-ol

Formula

C16 H16 N6 O

Formal charge

0

Molecular weight

308.338 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Nc3nccc(n2c1cc(C#CC(C)(O)CC)ncc1cn2)n3
SMILES CACTVS 3.385 CC[C](C)(O)C#Cc1cc2n(ncc2cn1)c3ccnc(N)n3
SMILES OpenEye OEToolkits 2.0.7 CCC(C)(C#Cc1cc2c(cn1)cnn2c3ccnc(n3)N)O
Canonical SMILES CACTVS 3.385 CC[C@](C)(O)C#Cc1cc2n(ncc2cn1)c3ccnc(N)n3
Canonical SMILES OpenEye OEToolkits 2.0.7 CC[C@@](C)(C#Cc1cc2c(cn1)cnn2c3ccnc(n3)N)O

IUPAC InChI

InChI=1S/C16H16N6O/c1-3-16(2,23)6-4-12-8-13-11(9-19-12)10-20-22(13)14-5-7-18-15(17)21-14/h5,7-10,23H,3H2,1-2H3,(H2,17,18,21)/t16-/m0/s1

IUPAC InChI key

WZLQQYUWMGFXDE-INIZCTEOSA-N
VSY

wwPDB Information

Atom count

39 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-09-11

Last modified at

2021-05-14

Status

Released

Obsoleted

Not Assigned



VSY : Atoms of Molecule

Total Number of Atoms: 39
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 -1.917 -3.664 -0.634
2 N3 N N2 N Y N 0 -2.701 0.931 -0.053
3 C4 C C1 N Y N 0 -3.138 -0.387 0.048
4 C8 C C5 N Y N 0 -0.19 3.436 -0.197
5 C5 C C2 N Y N 0 -1.393 1.338 -0.05
6 C6 C C3 N Y N 0 -1.404 2.746 -0.173
7 C7 C C4 N Y N 0 -2.807 3.136 -0.248
8 C10 C C6 N N N 0 2.268 0.805 0.104
9 C13 C C7 N N N 0 5.733 0.65 0.219
10 C15 C C8 N N N 0 6.137 -2.072 -0.786
11 C14 C C12 N N N 0 4.778 -1.377 -0.887
12 C1 C C9 N Y N 0 -2.762 -2.644 -0.233
13 C11 C C10 N N N 0 3.311 0.272 0.181
14 C12 C C11 S N N 0 4.619 -0.397 0.278
15 C16 C C13 N Y N 0 -0.165 0.692 0.042
16 C2 C C14 N Y N 0 -4.802 -1.999 0.625
17 C3 C C15 N Y N 0 -4.41 -0.675 0.541
18 C9 C C16 N Y N 0 0.996 1.456 0.009
19 N2 N N3 N Y N 0 -3.963 -2.947 0.237
20 N4 N N4 N Y N 0 -3.528 2.053 -0.18
21 N5 N N5 N Y N 0 0.947 2.783 -0.107
22 N6 N N6 N Y N 0 -2.35 -1.389 -0.328
23 O1 O O1 N N N 0 4.699 -1.11 1.514
24 H1 H H1 N N N 0 -2.206 -4.587 -0.569
25 H2 H H2 N N N 0 -1.036 -3.455 -0.984
26 H3 H H3 N N N 0 -3.182 4.144 -0.349
27 H4 H H4 N N N 0 -0.185 4.512 -0.291
28 H5 H H5 N N N 0 5.62 1.348 1.048
29 H6 H H6 N N N 0 6.701 0.154 0.291
30 H7 H H7 N N N 0 5.672 1.193 -0.724
31 H8 H H8 N N N 0 6.251 -2.77 -1.615
32 H9 H H9 N N N 0 6.931 -1.327 -0.828
33 H10 H H10 N N N 0 6.199 -2.616 0.157
34 H11 H H11 N N N 0 4.717 -0.834 -1.83
35 H12 H H12 N N N 0 3.984 -2.123 -0.845
36 H13 H H13 N N N 0 -0.115 -0.382 0.137
37 H14 H H14 N N N 0 -5.779 -2.256 1.007
38 H15 H H15 N N N 0 -5.075 0.118 0.851
39 H16 H H16 N N N 0 4.022 -1.791 1.62



VSY : Chemical Bonds

Total Number of Bonds: 41
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C7 N4 C N doub 1.3 N Y
2 C7 C6 C C sing 1.46 N Y
3 N4 N3 N N sing 1.4 N Y
4 C6 C8 C C doub 1.4 N Y
5 C6 C5 C C sing 1.41 N Y
6 C8 N5 C N sing 1.31 N Y
7 N3 C5 N C sing 1.37 N Y
8 N3 C4 N C sing 1.39 N N
9 C3 C4 C C doub 1.39 N Y
10 C3 C2 C C sing 1.38 N Y
11 C5 C16 C C doub 1.39 N Y
12 C4 N6 C N sing 1.33 N Y
13 C2 N2 C N doub 1.32 N Y
14 N5 C9 N C doub 1.33 N Y
15 C16 C9 C C sing 1.39 N Y
16 N6 C1 N C doub 1.32 N Y
17 N2 C1 N C sing 1.32 N Y
18 C9 C10 C C sing 1.43 N N
19 C1 N1 C N sing 1.38 N N
20 C10 C11 C C trip 1.17 N N
21 C11 C12 C C sing 1.47 N N
22 C13 C12 C C sing 1.53 N N
23 C12 O1 C O sing 1.43 N N
24 C12 C14 C C sing 1.53 N N
25 C14 C15 C C sing 1.53 N N
26 N1 H1 N H sing 0.97 N N
27 N1 H2 N H sing 0.97 N N
28 C7 H3 C H sing 1.08 N N
29 C8 H4 C H sing 1.08 N N
30 C13 H5 C H sing 1.09 N N
31 C13 H6 C H sing 1.09 N N
32 C13 H7 C H sing 1.09 N N
33 C15 H8 C H sing 1.09 N N
34 C15 H9 C H sing 1.09 N N
35 C15 H10 C H sing 1.09 N N
36 C14 H11 C H sing 1.09 N N
37 C14 H12 C H sing 1.09 N N
38 C16 H13 C H sing 1.08 N N
39 C2 H14 C H sing 1.08 N N
40 C3 H15 C H sing 1.08 N N
41 O1 H16 O H sing 0.97 N N



VSY : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
VSY 7jxy Open in New Window Bound ligand 2 1