Chemical Components in the PDB

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D42 : Summary

Code

D42

One-letter code

X

Molecule name

1-(3-(2,4-DIMETHYLTHIAZOL-5-YL)-4-OXO-2,4-DIHYDROINDENO[1,2-C]PYRAZOL-5-YL)-3-(4-METHYLPIPERAZIN-1-YL)UREA

Synonyms

DPH-042562

Systematic names

ProgramVersionName
ACDLabs 10.04 1-[3-(2,4-dimethyl-1,3-thiazol-5-yl)-4-oxo-2,4-dihydroindeno[1,2-c]pyrazol-5-yl]-3-(4-methylpiperazin-1-yl)urea
OpenEye OEToolkits 1.5.0 3-[3-(2,4-dimethyl-1,3-thiazol-5-yl)-4-oxo-2H-indeno[1,2-c]pyrazol-5-yl]-1-(4-methylpiperazin-1-yl)urea

Formula

C21 H23 N7 O2 S

Formal charge

0

Molecular weight

437.518 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(NN1CCN(C)CC1)Nc2cccc3c2C(=O)c4c(nnc34)c5sc(nc5C)C
SMILES CACTVS 3.341 CN1CCN(CC1)NC(=O)Nc2cccc3c4n[nH]c(c5sc(C)nc5C)c4C(=O)c23
SMILES OpenEye OEToolkits 1.5.0 Cc1c(sc(n1)C)c2c3c(n[nH]2)-c4cccc(c4C3=O)NC(=O)NN5CCN(CC5)C
Canonical SMILES CACTVS 3.341 CN1CCN(CC1)NC(=O)Nc2cccc3c4n[nH]c(c5sc(C)nc5C)c4C(=O)c23
Canonical SMILES OpenEye OEToolkits 1.5.0 Cc1c(sc(n1)C)c2c3c(n[nH]2)-c4cccc(c4C3=O)NC(=O)NN5CCN(CC5)C

IUPAC InChI

InChI=1S/C21H23N7O2S/c1-11-20(31-12(2)22-11)18-16-17(24-25-18)13-5-4-6-14(15(13)19(16)29)23-21(30)26-28-9-7-27(3)8-10-28/h4-6H,7-10H2,1-3H3,(H,24,25)(H2,23,26,30)

IUPAC InChI key

KRKQVGZXTNLQSV-UHFFFAOYSA-N
D42

wwPDB Information

Atom count

54 (31 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2005-09-28

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



D42 : 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 C1 C C1 N N N 0 4.23 2.98 0.622
2 C2 C C2 N N N 0 4.435 1.557 1.143
3 N3 N N3 N N N 0 4.127 0.593 0.079
4 C4 C C4 N N N 0 5.066 0.856 -1.019
5 C5 C C5 N N N 0 4.861 2.28 -1.54
6 N6 N N6 N N N 0 5.169 3.243 -0.476
7 C15 C C15 N N N 0 4.839 4.574 -1.004
8 N19 N N19 N N N 0 4.434 -0.644 0.57
9 C20 C C20 N N N 0 3.497 -1.612 0.591
10 N21 N N21 N N N 0 2.288 -1.392 0.037
11 C22 C C22 N Y N 0 1.363 -2.429 -0.049
12 C23 C C23 N Y N 0 1.798 -3.749 -0.122
13 C24 C C24 N Y N 0 0.884 -4.778 -0.207
14 C25 C C25 N Y N 0 -0.476 -4.512 -0.221
15 C26 C C26 N Y N 0 -0.933 -3.203 -0.148
16 C27 C C27 N Y N 0 -0.009 -2.147 -0.056
17 C31 C C31 N Y N 0 -2.305 -2.637 -0.143
18 C32 C C32 N Y N 0 -2.18 -1.179 -0.049
19 C33 C C33 N N N 0 -0.747 -0.87 0.002
20 N34 N N34 N Y N 0 -3.584 -2.917 -0.189
21 N35 N N35 N Y N 0 -4.327 -1.734 -0.13
22 C36 C C36 N Y N 0 -3.476 -0.67 -0.045
23 C37 C C37 N Y N 0 -3.855 0.745 0.036
24 S38 S S38 N Y N 0 -3.149 2.064 1.013
25 C39 C C39 N Y N 0 -4.205 3.333 0.476
26 N40 N N40 N Y N 0 -4.992 2.706 -0.372
27 C41 C C41 N Y N 0 -4.852 1.428 -0.625
28 C42 C C42 N N N 0 -5.762 0.725 -1.6
29 C46 C C46 N N N 0 -4.217 4.785 0.879
30 O47 O O47 N N N 0 3.741 -2.683 1.112
31 O50 O O50 N N N 0 -0.255 0.241 0.083
32 H11 H 1H1 N N N 0 4.408 3.691 1.429
33 H12 H 2H1 N N N 0 3.208 3.091 0.26
34 H21A H 1H2 N N N 0 3.774 1.383 1.992
35 H22 H 2H2 N N N 0 5.471 1.431 1.458
36 H41 H 1H4 N N N 0 4.888 0.146 -1.826
37 H42 H 2H4 N N N 0 6.088 0.746 -0.657
38 H51 H 1H5 N N N 0 3.826 2.405 -1.855
39 H52 H 2H5 N N N 0 5.522 2.453 -2.389
40 H151 H 1H15 N N N 0 3.781 4.609 -1.265
41 H152 H 2H15 N N N 0 5.051 5.328 -0.246
42 H153 H 3H15 N N N 0 5.439 4.772 -1.892
43 H19 H H19 N N N 0 5.327 -0.826 0.902
44 H21 H H21 N N N 0 2.063 -0.512 -0.303
45 H23 H H23 N N N 0 2.856 -3.968 -0.113
46 H24 H H24 N N N 0 1.23 -5.799 -0.264
47 H25 H H25 N N N 0 -1.183 -5.326 -0.288
48 H35 H H35 N N N 0 -5.295 -1.678 -0.148
49 H421 H 1H42 N N N 0 -5.333 0.779 -2.6
50 H422 H 2H42 N N N 0 -5.871 -0.319 -1.306
51 H423 H 3H42 N N N 0 -6.739 1.208 -1.597
52 H461 H 1H46 N N N 0 -3.569 5.353 0.211
53 H462 H 2H46 N N N 0 -5.234 5.172 0.814
54 H463 H 3H46 N N N 0 -3.857 4.881 1.903



D42 : Chemical Bonds

Total Number of Bonds: 58
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.53 N N
2 C1 N6 C N sing 1.47 N N
3 C1 H11 C H sing 1.09 N N
4 C1 H12 C H sing 1.09 N N
5 C2 N3 C N sing 1.47 N N
6 C2 H21A C H sing 1.09 N N
7 C2 H22 C H sing 1.09 N N
8 N3 C4 N C sing 1.47 N N
9 N3 N19 N N sing 1.37 N N
10 C4 C5 C C sing 1.53 N N
11 C4 H41 C H sing 1.09 N N
12 C4 H42 C H sing 1.09 N N
13 C5 N6 C N sing 1.47 N N
14 C5 H51 C H sing 1.09 N N
15 C5 H52 C H sing 1.09 N N
16 N6 C15 N C sing 1.47 N N
17 C15 H151 C H sing 1.09 N N
18 C15 H152 C H sing 1.09 N N
19 C15 H153 C H sing 1.09 N N
20 N19 C20 N C sing 1.35 N N
21 N19 H19 N H sing 0.97 N N
22 C20 N21 C N sing 1.35 N N
23 C20 O47 C O doub 1.22 N N
24 N21 C22 N C sing 1.39 N N
25 N21 H21 N H sing 0.97 N N
26 C22 C23 C C doub 1.39 N Y
27 C22 C27 C C sing 1.4 N Y
28 C23 C24 C C sing 1.38 N Y
29 C23 H23 C H sing 1.08 N N
30 C24 C25 C C doub 1.39 N Y
31 C24 H24 C H sing 1.08 N N
32 C25 C26 C C sing 1.39 N Y
33 C25 H25 C H sing 1.08 N N
34 C26 C27 C C doub 1.41 N Y
35 C26 C31 C C sing 1.48 N Y
36 C27 C33 C C sing 1.48 N N
37 C31 C32 C C sing 1.47 N Y
38 C31 N34 C N doub 1.31 N Y
39 C32 C33 C C sing 1.47 N N
40 C32 C36 C C doub 1.39 N Y
41 C33 O50 C O doub 1.22 N N
42 N34 N35 N N sing 1.4 N Y
43 N35 C36 N C sing 1.37 N Y
44 N35 H35 N H sing 0.97 N N
45 C36 C37 C C sing 1.47 N Y
46 C37 S38 C S sing 1.79 N Y
47 C37 C41 C C doub 1.38 N Y
48 S38 C39 S C sing 1.74 N Y
49 C39 N40 C N doub 1.32 N Y
50 C39 C46 C C sing 1.51 N N
51 N40 C41 N C sing 1.31 N Y
52 C41 C42 C C sing 1.51 N N
53 C42 H421 C H sing 1.09 N N
54 C42 H422 C H sing 1.09 N N
55 C42 H423 C H sing 1.09 N N
56 C46 H461 C H sing 1.09 N N
57 C46 H462 C H sing 1.09 N N
58 C46 H463 C H sing 1.09 N N



D42 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
D42 2b52 Open in New Window Bound ligand 1 1