Chemical Components in the PDB

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XYJ : Summary

Code

XYJ

One-letter code

X

Molecule name

3-[(1,3-dimethyl-2,6-dioxo-2,3,6,9-tetrahydro-1H-purin-8-yl)sulfanyl]-N-{[2-(morpholin-4-yl)ethyl]sulfonyl}propanamide

Systematic names

ProgramVersionName
ACDLabs 12.01 3-[(1,3-dimethyl-2,6-dioxo-2,3,6,9-tetrahydro-1H-purin-8-yl)sulfanyl]-N-{[2-(morpholin-4-yl)ethyl]sulfonyl}propanamide
OpenEye OEToolkits 2.0.7 3-[[1,3-dimethyl-2,6-bis(oxidanylidene)-9~{H}-purin-8-yl]sulfanyl]-~{N}-(2-morpholin-4-ylethylsulfonyl)propanamide

Formula

C16 H24 N6 O6 S2

Formal charge

0

Molecular weight

460.528 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C(NS(CCN1CCOCC1)(=O)=O)(CCSc3nc2c(C(N(C(N2C)=O)C)=O)n3)=O
SMILES CACTVS 3.385 CN1C(=O)N(C)c2[nH]c(SCCC(=O)N[S](=O)(=O)CCN3CCOCC3)nc2C1=O
SMILES OpenEye OEToolkits 2.0.7 CN1c2c(nc([nH]2)SCCC(=O)NS(=O)(=O)CCN3CCOCC3)C(=O)N(C1=O)C
Canonical SMILES CACTVS 3.385 CN1C(=O)N(C)c2[nH]c(SCCC(=O)N[S](=O)(=O)CCN3CCOCC3)nc2C1=O
Canonical SMILES OpenEye OEToolkits 2.0.7 CN1c2c(nc([nH]2)SCCC(=O)NS(=O)(=O)CCN3CCOCC3)C(=O)N(C1=O)C

IUPAC InChI

InChI=1S/C16H24N6O6S2/c1-20-13-12(14(24)21(2)16(20)25)17-15(18-13)29-9-3-11(23)19-30(26,27)10-6-22-4-7-28-8-5-22/h3-10H2,1-2H3,(H,17,18)(H,19,23)

IUPAC InChI key

JUFGUKJIZDHLKW-UHFFFAOYSA-N
XYJ

wwPDB Information

Atom count

54 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-01-20

Last modified at

2021-02-12

Status

Released

Obsoleted

Not Assigned



XYJ : Atoms of Molecule

Total Number of Atoms: 54
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N N N 0 -1.657 2.031 -0.187
2 C13 C C2 N N N 0 -4.446 0.403 -0.023
3 C17 C C3 N N N 0 -6.455 -2.714 2.14
4 C20 C C4 N N N 0 -6.858 -2.409 -0.668
5 C26 C C5 N N N 0 7.688 0.522 1.304
6 C02 C C6 N N N 0 4.809 -1.68 -0.856
7 C03 C C7 N Y N 0 4.408 -0.448 -0.176
8 C04 C C8 N Y N 0 5.372 0.259 0.528
9 C06 C C9 N Y N 0 3.431 1.294 0.678
10 C08 C C10 N N N 0 0.764 1.753 0.271
11 C09 C C11 N N N 0 -0.464 2.633 0.51
12 C14 C C12 N N N 0 -5.647 -0.312 -0.647
13 C16 C C13 N N N 0 -6.29 -1.363 1.438
14 C19 C C14 N N N 0 -7.018 -3.75 0.054
15 C27 C C15 N N N 0 6.994 -1.354 -0.074
16 C29 C C16 N N N 0 6.523 -3.305 -1.441
17 N05 N N1 N Y N 0 4.745 1.348 1.057
18 N11 N N2 N N N 0 -2.858 2.639 -0.114
19 N15 N N3 N N N 0 -5.872 -1.587 0.047
20 N24 N N4 N Y N 0 3.235 0.226 -0.054
21 O18 O O2 N N N 0 -7.395 -3.511 1.413
22 N25 N N5 N N N 0 6.663 -0.218 0.563
23 N28 N N6 N N N 0 6.098 -2.074 -0.769
24 O01 O O1 N N N 0 3.997 -2.338 -1.482
25 O21 O O3 N N N 0 -3.72 1.75 -2.209
26 O22 O O4 N N N 0 -5.227 2.886 -0.61
27 O23 O O5 N N N 0 -1.536 1.002 -0.817
28 O30 O O6 N N N 0 8.145 -1.743 -0.021
29 S07 S S1 N N N 0 2.197 2.476 1.108
30 S12 S S2 N N N 0 -4.168 1.978 -0.88
31 H1 H H1 N N N 0 -4.644 0.593 1.031
32 H2 H H2 N N N 0 -3.56 -0.224 -0.119
33 H3 H H3 N N N 0 -5.494 -3.226 2.175
34 H4 H H4 N N N 0 -6.82 -2.555 3.155
35 H5 H H5 N N N 0 -6.516 -2.584 -1.688
36 H6 H H6 N N N 0 -7.817 -1.891 -0.69
37 H7 H H7 N N N 0 7.72 0.167 2.333
38 H8 H H8 N N N 0 8.659 0.365 0.835
39 H9 H H9 N N N 0 7.447 1.585 1.293
40 H10 H H10 N N N 0 0.578 0.754 0.666
41 H11 H H11 N N N 0 0.962 1.689 -0.799
42 H12 H H12 N N N 0 -0.278 3.632 0.114
43 H13 H H13 N N N 0 -0.663 2.697 1.58
44 H14 H H14 N N N 0 -6.533 0.315 -0.551
45 H15 H H15 N N N 0 -5.448 -0.502 -1.702
46 H16 H H16 N N N 0 -7.24 -0.828 1.451
47 H17 H H17 N N N 0 -5.534 -0.774 1.957
48 H18 H H18 N N N 0 -7.79 -4.34 -0.439
49 H19 H H19 N N N 0 -6.072 -4.292 0.029
50 H20 H H20 N N N 0 5.671 -3.754 -1.95
51 H21 H H21 N N N 0 7.3 -3.071 -2.169
52 H22 H H22 N N N 0 6.916 -4.004 -0.703
53 H23 H H23 N N N 0 5.156 2.036 1.604
54 H24 H H24 N N N 0 -2.954 3.464 0.387



XYJ : Chemical Bonds

Total Number of Bonds: 56
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C19 O18 C O sing 1.43 N N
2 C19 C20 C C sing 1.53 N N
3 O18 C17 O C sing 1.43 N N
4 C20 N15 C N sing 1.47 N N
5 C17 C16 C C sing 1.53 N N
6 N15 C16 N C sing 1.47 N N
7 N15 C14 N C sing 1.47 N N
8 C14 C13 C C sing 1.53 N N
9 C13 S12 C S sing 1.81 N N
10 O22 S12 O S doub 1.42 N N
11 O01 C02 O C doub 1.22 N N
12 O23 C10 O C doub 1.21 N N
13 S12 O21 S O doub 1.42 N N
14 S12 N11 S N sing 1.66 N N
15 N24 C03 N C sing 1.36 N Y
16 N24 C06 N C doub 1.31 N Y
17 C02 C03 C C sing 1.46 N N
18 C02 N28 C N sing 1.35 N N
19 C29 N28 C N sing 1.47 N N
20 C10 N11 C N sing 1.35 N N
21 C10 C09 C C sing 1.51 N N
22 C03 C04 C C doub 1.39 N Y
23 S07 C06 S C sing 1.76 N N
24 S07 C08 S C sing 1.81 N N
25 N28 C27 N C sing 1.34 N N
26 C06 N05 C N sing 1.37 N Y
27 C09 C08 C C sing 1.53 N N
28 C04 N05 C N sing 1.36 N Y
29 C04 N25 C N sing 1.38 N N
30 C27 N25 C N sing 1.34 N N
31 C27 O30 C O doub 1.22 N N
32 N25 C26 N C sing 1.47 N N
33 C13 H1 C H sing 1.09 N N
34 C13 H2 C H sing 1.09 N N
35 C17 H3 C H sing 1.09 N N
36 C17 H4 C H sing 1.09 N N
37 C20 H5 C H sing 1.09 N N
38 C20 H6 C H sing 1.09 N N
39 C26 H7 C H sing 1.09 N N
40 C26 H8 C H sing 1.09 N N
41 C26 H9 C H sing 1.09 N N
42 C08 H10 C H sing 1.09 N N
43 C08 H11 C H sing 1.09 N N
44 C09 H12 C H sing 1.09 N N
45 C09 H13 C H sing 1.09 N N
46 C14 H14 C H sing 1.09 N N
47 C14 H15 C H sing 1.09 N N
48 C16 H16 C H sing 1.09 N N
49 C16 H17 C H sing 1.09 N N
50 C19 H18 C H sing 1.09 N N
51 C19 H19 C H sing 1.09 N N
52 C29 H20 C H sing 1.09 N N
53 C29 H21 C H sing 1.09 N N
54 C29 H22 C H sing 1.09 N N
55 N05 H23 N H sing 0.97 N N
56 N11 H24 N H sing 0.97 N N



XYJ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
XYJ 7lg7 Open in New Window Bound ligand 1 1