Chemical Components in the PDB

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WYJ : Summary

Code

WYJ

One-letter code

X

Molecule name

[(2S,6R)-6-methyl-4-(9H-pyrimido[4,5-b]indol-4-yl)morpholin-2-yl]methanol

Systematic names

ProgramVersionName
ACDLabs 12.01 [(2S,6R)-6-methyl-4-(9H-pyrimido[4,5-b]indol-4-yl)morpholin-2-yl]methanol
OpenEye OEToolkits 2.0.7 [(2~{S},6~{R})-6-methyl-4-(9~{H}-pyrimido[4,5-b]indol-4-yl)morpholin-2-yl]methanol

Formula

C16 H18 N4 O2

Formal charge

0

Molecular weight

298.34 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c4cc2c(c1c(ncnc1n2)N3CC(C)OC(CO)C3)cc4
SMILES CACTVS 3.385 C[CH]1CN(C[CH](CO)O1)c2ncnc3[nH]c4ccccc4c23
SMILES OpenEye OEToolkits 2.0.7 CC1CN(CC(O1)CO)c2c3c4ccccc4[nH]c3ncn2
Canonical SMILES CACTVS 3.385 C[C@@H]1CN(C[C@@H](CO)O1)c2ncnc3[nH]c4ccccc4c23
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@@H]1CN(C[C@H](O1)CO)c2c3c4ccccc4[nH]c3ncn2

IUPAC InChI

InChI=1S/C16H18N4O2/c1-10-6-20(7-11(8-21)22-10)16-14-12-4-2-3-5-13(12)19-15(14)17-9-18-16/h2-5,9-11,21H,6-8H2,1H3,(H,17,18,19)/t10-,11+/m1/s1

IUPAC InChI key

SSHCMXMCAMBDLI-MNOVXSKESA-N
WYJ

wwPDB Information

Atom count

40 (22 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-11-17

Last modified at

2022-07-08

Status

Released

Obsoleted

Not Assigned



WYJ : Atoms of Molecule

Total Number of Atoms: 40
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N Y N 0 -3.34 3.053 0.399
2 C21 C C2 N N N 0 2.62 1.623 -1.1
3 C01 C C3 N N N 0 3.852 -0.495 2.404
4 C02 C C4 R N N 0 3.0 -0.06 1.21
5 C03 C C5 N N N 0 1.75 -0.939 1.127
6 C05 C C6 N Y N 0 -0.194 -1.305 -0.146
7 C06 C C7 N Y N 0 -1.443 -0.679 -0.066
8 C07 C C8 N Y N 0 -1.893 0.711 0.101
9 C08 C C9 N Y N 0 -3.296 0.673 0.104
10 C09 C C10 N Y N 0 -4.01 1.858 0.248
11 C11 C C11 N Y N 0 -1.954 3.089 0.402
12 C12 C C12 N Y N 0 -1.229 1.927 0.255
13 C14 C C13 N Y N 0 -2.601 -1.467 -0.154
14 C16 C C14 N Y N 0 -1.267 -3.332 -0.382
15 C18 C C15 N N N 0 1.783 -0.725 -1.283
16 C19 C C16 S N N 0 3.033 0.152 -1.176
17 N04 N N1 N N N 0 0.974 -0.567 -0.065
18 N13 N N2 N Y N 0 -3.695 -0.644 -0.051
19 N15 N N3 N Y N 0 -2.462 -2.784 -0.311
20 N17 N N4 N Y N 0 -0.155 -2.626 -0.303
21 O20 O O1 N N N 0 3.758 -0.202 0.006
22 O22 O O2 N N N 0 3.788 2.447 -1.117
23 H101 H H1 N N N 0 -3.9 3.97 0.511
24 H211 H H2 N N N 0 1.99 1.868 -1.955
25 H212 H H3 N N N 0 2.066 1.798 -0.178
26 H012 H H4 N N N 0 4.149 -1.536 2.279
27 H013 H H5 N N N 0 4.743 0.132 2.463
28 H011 H H6 N N N 0 3.273 -0.389 3.322
29 H021 H H7 N N N 0 2.705 0.982 1.334
30 H032 H H8 N N N 0 2.045 -1.986 1.058
31 H031 H H9 N N N 0 1.14 -0.79 2.019
32 H091 H H10 N N N 0 -5.09 1.842 0.243
33 H111 H H11 N N N 0 -1.441 4.032 0.521
34 H121 H H12 N N N 0 -0.15 1.957 0.258
35 H161 H H13 N N N 0 -1.195 -4.402 -0.509
36 H182 H H14 N N N 0 1.198 -0.421 -2.15
37 H181 H H15 N N N 0 2.078 -1.769 -1.391
38 H191 H H16 N N N 0 3.664 -0.005 -2.051
39 H131 H H17 N N N 0 -4.618 -0.943 -0.081
40 H221 H H18 N N N 0 3.601 3.395 -1.072



WYJ : Chemical Bonds

Total Number of Bonds: 43
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O22 C21 O C sing 1.43 N N
2 O20 C19 O C sing 1.43 N N
3 O20 C02 O C sing 1.43 N N
4 C01 C02 C C sing 1.53 N N
5 C21 C19 C C sing 1.53 N N
6 C19 C18 C C sing 1.53 N N
7 C02 C03 C C sing 1.53 N N
8 C18 N04 C N sing 1.47 N N
9 C03 N04 C N sing 1.47 N N
10 N04 C05 N C sing 1.38 N N
11 C12 C11 C C doub 1.38 N Y
12 C12 C07 C C sing 1.39 N Y
13 C11 C10 C C sing 1.39 N Y
14 C05 N17 C N doub 1.33 N Y
15 C05 C06 C C sing 1.4 N Y
16 C07 C06 C C sing 1.47 N Y
17 C07 C08 C C doub 1.4 N Y
18 C10 C09 C C doub 1.38 N Y
19 N17 C16 N C sing 1.32 N Y
20 C06 C14 C C doub 1.4 N Y
21 C08 C09 C C sing 1.39 N Y
22 C08 N13 C N sing 1.38 N Y
23 C16 N15 C N doub 1.32 N Y
24 C14 N13 C N sing 1.37 N Y
25 C14 N15 C N sing 1.33 N Y
26 C10 H101 C H sing 1.08 N N
27 C21 H211 C H sing 1.09 N N
28 C21 H212 C H sing 1.09 N N
29 C01 H012 C H sing 1.09 N N
30 C01 H013 C H sing 1.09 N N
31 C01 H011 C H sing 1.09 N N
32 C02 H021 C H sing 1.09 N N
33 C03 H032 C H sing 1.09 N N
34 C03 H031 C H sing 1.09 N N
35 C09 H091 C H sing 1.08 N N
36 C11 H111 C H sing 1.08 N N
37 C12 H121 C H sing 1.08 N N
38 C16 H161 C H sing 1.08 N N
39 C18 H182 C H sing 1.09 N N
40 C18 H181 C H sing 1.09 N N
41 C19 H191 C H sing 1.09 N N
42 N13 H131 N H sing 0.97 N N
43 O22 H221 O H sing 0.97 N N



WYJ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
WYJ 5sp3 Open in New Window Bound ligand 1 1