Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

D3B : Summary

Code

D3B

One-letter code

X

Molecule name

1-(2,5-dimethylphenyl)-3-(2-oxidanyl-5-sulfamoyl-phenyl)urea

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 1-(2,5-dimethylphenyl)-3-(2-oxidanyl-5-sulfamoyl-phenyl)urea

Formula

C15 H17 N3 O4 S

Formal charge

0

Molecular weight

335.378 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Cc1ccc(C)c(NC(=O)Nc2cc(ccc2O)[S](N)(=O)=O)c1
SMILES OpenEye OEToolkits 2.0.6 Cc1ccc(c(c1)NC(=O)Nc2cc(ccc2O)S(=O)(=O)N)C
Canonical SMILES CACTVS 3.385 Cc1ccc(C)c(NC(=O)Nc2cc(ccc2O)[S](N)(=O)=O)c1
Canonical SMILES OpenEye OEToolkits 2.0.6 Cc1ccc(c(c1)NC(=O)Nc2cc(ccc2O)S(=O)(=O)N)C

IUPAC InChI

InChI=1S/C15H17N3O4S/c1-9-3-4-10(2)12(7-9)17-15(20)18-13-8-11(23(16,21)22)5-6-14(13)19/h3-8,19H,1-2H3,(H2,16,21,22)(H2,17,18,20)

IUPAC InChI key

ITJAYNQSUKWUOO-UHFFFAOYSA-N
D3B

wwPDB Information

Atom count

40 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-12-15

Last modified at

2018-10-05

Status

Released

Obsoleted

Not Assigned



D3B : 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 C3 C C1 N Y N 0 3.49 2.311 0.335
2 C4 C C2 N Y N 0 3.917 0.998 0.273
3 C5 C C3 N Y N 0 3.019 -0.012 -0.022
4 C6 C C4 N Y N 0 1.69 0.287 -0.257
5 C7 C C5 N Y N 0 -3.323 0.298 -0.24
6 C8 C C6 N Y N 0 -3.047 -1.062 -0.29
7 N20 N N1 N N N 0 -2.323 1.228 -0.548
8 C22 C C7 N N N 0 -1.042 0.974 -0.218
9 O23 O O1 N N N 0 -0.741 -0.099 0.27
10 N24 N N2 N N N 0 -0.094 1.908 -0.428
11 C1 C C8 N Y N 0 1.255 1.603 -0.197
12 C2 C C9 N Y N 0 2.158 2.619 0.106
13 C9 C C10 N Y N 0 -4.037 -1.977 0.009
14 C10 C C11 N Y N 0 -5.302 -1.541 0.358
15 C11 C C12 N Y N 0 -5.58 -0.187 0.408
16 C12 C C13 N Y N 0 -4.594 0.733 0.111
17 O1 O O2 N N N 0 1.735 3.909 0.179
18 S2 S S1 N N N 0 3.57 -1.683 -0.1
19 O3 O O3 N N N 0 2.642 -2.375 -0.924
20 O4 O O4 N N N 0 4.964 -1.634 -0.371
21 N5 N N3 N N N 0 3.413 -2.322 1.42
22 C13 C C14 N N N 0 -4.899 2.208 0.161
23 C14 C C15 N N N 0 -3.739 -3.454 -0.046
24 H1 H H1 N N N 0 4.194 3.097 0.566
25 H2 H H2 N N N 0 4.954 0.759 0.455
26 H3 H H3 N N N 0 0.991 -0.503 -0.488
27 H4 H H4 N N N 0 -2.06 -1.404 -0.563
28 H5 H H5 N N N 0 -2.553 2.055 -0.999
29 H6 H H6 N N N 0 -0.344 2.792 -0.74
30 H7 H H7 N N N 0 -6.075 -2.258 0.591
31 H8 H H8 N N N 0 -6.569 0.151 0.681
32 H9 H H9 N N N 0 1.441 4.178 1.06
33 H10 H H10 N N N 0 3.236 -3.27 1.532
34 H11 H H11 N N N 0 3.497 -1.749 2.198
35 H12 H H12 N N N 0 -5.254 2.539 -0.815
36 H13 H H13 N N N 0 -5.669 2.395 0.909
37 H14 H H14 N N N 0 -3.995 2.758 0.424
38 H15 H H15 N N N 0 -3.947 -3.829 -1.048
39 H16 H H16 N N N 0 -2.69 -3.621 0.195
40 H17 H H17 N N N 0 -4.366 -3.978 0.676



D3B : 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 C14 C9 C C sing 1.51 N N
2 C9 C10 C C doub 1.38 N Y
3 C9 C8 C C sing 1.38 N Y
4 C10 C11 C C sing 1.38 N Y
5 C8 C7 C C doub 1.39 N Y
6 O23 C22 O C doub 1.22 N N
7 C11 C12 C C doub 1.38 N Y
8 C7 C12 C C sing 1.39 N Y
9 C7 N20 C N sing 1.4 N N
10 C22 N20 C N sing 1.35 N N
11 C22 N24 C N sing 1.35 N N
12 C12 C13 C C sing 1.51 N N
13 N24 C1 N C sing 1.4 N N
14 O1 C2 O C sing 1.36 N N
15 C1 C2 C C doub 1.39 N Y
16 C1 C6 C C sing 1.39 N Y
17 C2 C3 C C sing 1.39 N Y
18 C6 C5 C C doub 1.38 N Y
19 C3 C4 C C doub 1.38 N Y
20 C5 C4 C C sing 1.38 N Y
21 C5 S2 C S sing 1.76 N N
22 N5 S2 N S sing 1.66 N N
23 S2 O4 S O doub 1.42 N N
24 S2 O3 S O doub 1.42 N N
25 C3 H1 C H sing 1.08 N N
26 C4 H2 C H sing 1.08 N N
27 C6 H3 C H sing 1.08 N N
28 C8 H4 C H sing 1.08 N N
29 N20 H5 N H sing 0.97 N N
30 N24 H6 N H sing 0.97 N N
31 C10 H7 C H sing 1.08 N N
32 C11 H8 C H sing 1.08 N N
33 O1 H9 O H sing 0.97 N N
34 N5 H10 N H sing 0.97 N N
35 N5 H11 N H sing 0.97 N N
36 C13 H12 C H sing 1.09 N N
37 C13 H13 C H sing 1.09 N N
38 C13 H14 C H sing 1.09 N N
39 C14 H15 C H sing 1.09 N N
40 C14 H16 C H sing 1.09 N N
41 C14 H17 C H sing 1.09 N N



D3B : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
D3B 6faf Open in New Window Bound ligand 2 1