Chemical Components in the PDB

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VMJ : Summary

Code

VMJ

One-letter code

X

Molecule name

5-[4-(hydroxymethyl)phenyl]-1-methyl-6-{[(1R)-1-phenylethyl]sulfanyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one

Systematic names

ProgramVersionName
ACDLabs 12.01 5-[4-(hydroxymethyl)phenyl]-1-methyl-6-{[(1R)-1-phenylethyl]sulfanyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
OpenEye OEToolkits 2.0.7 5-[4-(hydroxymethyl)phenyl]-1-methyl-6-[(1~{R})-1-phenylethyl]sulfanyl-pyrazolo[3,4-d]pyrimidin-4-one

Formula

C21 H20 N4 O2 S

Formal charge

0

Molecular weight

392.474 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C2N(c1ccc(cc1)CO)C(=Nc3c2cnn3C)SC(C)c4ccccc4
SMILES CACTVS 3.385 C[CH](SC1=Nc2n(C)ncc2C(=O)N1c3ccc(CO)cc3)c4ccccc4
SMILES OpenEye OEToolkits 2.0.7 CC(c1ccccc1)SC2=Nc3c(cnn3C)C(=O)N2c4ccc(cc4)CO
Canonical SMILES CACTVS 3.385 C[C@@H](SC1=Nc2n(C)ncc2C(=O)N1c3ccc(CO)cc3)c4ccccc4
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@H](c1ccccc1)SC2=Nc3c(cnn3C)C(=O)N2c4ccc(cc4)CO

IUPAC InChI

InChI=1S/C21H20N4O2S/c1-14(16-6-4-3-5-7-16)28-21-23-19-18(12-22-24(19)2)20(27)25(21)17-10-8-15(13-26)9-11-17/h3-12,14,26H,13H2,1-2H3/t14-/m1/s1

IUPAC InChI key

CXENUIKHQIZUDG-CQSZACIVSA-N
VMJ

wwPDB Information

Atom count

48 (28 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-08-27

Last modified at

2020-12-25

Status

Released

Obsoleted

Not Assigned



VMJ : Atoms of Molecule

Total Number of Atoms: 48
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O11 O O1 N N N 0 -3.744 -1.112 0.084
2 C1 C C1 N N N 0 -2.923 -0.212 0.062
3 N2 N N1 N N N 0 -1.599 -0.482 0.038
4 C12 C C2 N Y N 0 -1.158 -1.812 0.038
5 C13 C C3 N Y N 0 -0.96 -2.479 -1.163
6 C14 C C4 N Y N 0 -0.525 -3.79 -1.16
7 C15 C C5 N Y N 0 -0.287 -4.438 0.038
8 C27 C C6 N N N 0 0.186 -5.869 0.037
9 O27 O O2 N N N 0 1.615 -5.898 0.013
10 C16 C C7 N Y N 0 -0.483 -3.777 1.236
11 C17 C C8 N Y N 0 -0.913 -2.464 1.239
12 C3 C C9 N N N 0 -0.688 0.537 0.014
13 N4 N N2 N N N 0 -1.053 1.799 0.014
14 C5 C C10 N Y N 0 -2.347 2.147 0.037
15 N9 N N3 N Y N 0 -3.003 3.338 0.043
16 C10 C C11 N N N 0 -2.378 4.662 0.023
17 N8 N N4 N Y N 0 -4.379 3.081 0.072
18 C7 C C12 N Y N 0 -4.583 1.794 0.084
19 C6 C C13 N Y N 0 -3.332 1.145 0.056
20 S18 S S1 N N N 0 1.03 0.145 -0.018
21 C19 C C14 R N N 0 1.732 1.813 -0.042
22 C22 C C18 N Y N 0 5.328 0.981 -0.835
23 C26 C C15 N N N 0 1.342 2.512 -1.347
24 C20 C C16 N Y N 0 3.234 1.728 0.052
25 C21 C C17 N Y N 0 3.95 1.055 -0.919
26 C23 C C19 N Y N 0 5.99 1.58 0.22
27 C24 C C20 N Y N 0 5.273 2.254 1.191
28 C25 C C21 N Y N 0 3.895 2.327 1.108
29 H1 H H1 N N N 0 -1.146 -1.974 -2.099
30 H2 H H2 N N N 0 -0.371 -4.31 -2.095
31 H3 H H3 N N N 0 -0.171 -6.371 0.937
32 H4 H H4 N N N 0 -0.202 -6.38 -0.843
33 H5 H H5 N N N 0 1.991 -6.789 0.011
34 H6 H H6 N N N 0 -0.296 -4.286 2.17
35 H7 H H7 N N N 0 -1.062 -1.946 2.175
36 H8 H H8 N N N 0 -2.243 4.985 -1.01
37 H9 H H9 N N N 0 -3.016 5.374 0.545
38 H10 H H10 N N N 0 -1.407 4.614 0.517
39 H11 H H11 N N N 0 -5.547 1.307 0.106
40 H12 H H12 N N N 0 1.347 2.382 0.804
41 H13 H H13 N N N 0 1.765 3.516 -1.362
42 H14 H H14 N N N 0 1.728 1.943 -2.193
43 H15 H H15 N N N 0 0.256 2.573 -1.415
44 H16 H H16 N N N 0 3.434 0.586 -1.744
45 H17 H H17 N N N 0 5.888 0.454 -1.594
46 H18 H H18 N N N 0 7.066 1.522 0.286
47 H20 H H20 N N N 0 3.336 2.857 1.865
48 H19 H H19 N N N 0 5.79 2.723 2.016



VMJ : Chemical Bonds

Total Number of Bonds: 51
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C22 C23 C C doub 1.38 N Y
2 C22 C21 C C sing 1.38 N Y
3 C23 C24 C C sing 1.38 N Y
4 C21 C20 C C doub 1.38 N Y
5 C24 C25 C C doub 1.38 N Y
6 C20 C25 C C sing 1.38 N Y
7 C20 C19 C C sing 1.51 N N
8 C19 C26 C C sing 1.53 N N
9 C19 S18 C S sing 1.81 N N
10 C10 N9 C N sing 1.46 N N
11 S18 C3 S C sing 1.76 N N
12 N4 C3 N C doub 1.31 N N
13 N4 C5 N C sing 1.34 N N
14 N9 C5 N C sing 1.36 N Y
15 N9 N8 N N sing 1.4 N Y
16 C3 N2 C N sing 1.37 N N
17 C5 C6 C C doub 1.41 N Y
18 N8 C7 N C doub 1.3 N Y
19 N2 C12 N C sing 1.4 N N
20 N2 C1 N C sing 1.35 N N
21 C6 C7 C C sing 1.41 N Y
22 C6 C1 C C sing 1.42 N N
23 C13 C12 C C doub 1.39 N Y
24 C13 C14 C C sing 1.38 N Y
25 C12 C17 C C sing 1.39 N Y
26 C14 C15 C C doub 1.38 N Y
27 C1 O11 C O doub 1.22 N N
28 C17 C16 C C doub 1.38 N Y
29 C15 C16 C C sing 1.38 N Y
30 C15 C27 C C sing 1.51 N N
31 C27 O27 C O sing 1.43 N N
32 C13 H1 C H sing 1.08 N N
33 C14 H2 C H sing 1.08 N N
34 C27 H3 C H sing 1.09 N N
35 C27 H4 C H sing 1.09 N N
36 O27 H5 O H sing 0.97 N N
37 C16 H6 C H sing 1.08 N N
38 C17 H7 C H sing 1.08 N N
39 C10 H8 C H sing 1.09 N N
40 C10 H9 C H sing 1.09 N N
41 C10 H10 C H sing 1.09 N N
42 C7 H11 C H sing 1.08 N N
43 C19 H12 C H sing 1.09 N N
44 C26 H13 C H sing 1.09 N N
45 C26 H14 C H sing 1.09 N N
46 C26 H15 C H sing 1.09 N N
47 C21 H16 C H sing 1.08 N N
48 C22 H17 C H sing 1.08 N N
49 C23 H18 C H sing 1.08 N N
50 C24 H19 C H sing 1.08 N N
51 C25 H20 C H sing 1.08 N N



VMJ : Used in PDB Entries

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