Chemical Components in the PDB

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627 : Summary

Code

627

One-letter code

X

Molecule name

N-[(3E)-5-[(2R)-2-METHOXY-2-PHENYLACETYL]PYRROLO[3,4-C]PYRAZOL-3(5H)-YLIDENE]-4-(4-METHYLPIPERAZIN-1-YL)BENZAMIDE

Synonyms

Danusertib
PHA-739358

Systematic names

ProgramVersionName
ACDLabs 10.04 N-[(3E)-5-[(2R)-2-methoxy-2-phenylacetyl]pyrrolo[3,4-c]pyrazol-3(5H)-ylidene]-4-(4-methylpiperazin-1-yl)benzamide
OpenEye OEToolkits 1.7.6 N-[5-[(2R)-2-methoxy-2-phenyl-ethanoyl]-4,6-dihydro-1H-pyrrolo[3,4-c]pyrazol-3-yl]-4-(4-methylpiperazin-1-yl)benzamide

Formula

C26 H30 N6 O3

Formal charge

0

Molecular weight

474.555 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(n4cc3c(N=N/C3=N/C(=O)c1ccc(cc1)N2CCN(C)CC2)c4)C(OC)c5ccccc5
SMILES CACTVS 3.385 CO[CH](C(=O)N1Cc2[nH]nc(NC(=O)c3ccc(cc3)N4CCN(C)CC4)c2C1)c5ccccc5
SMILES OpenEye OEToolkits 1.7.6 CN1CCN(CC1)c2ccc(cc2)C(=O)Nc3c4c([nH]n3)CN(C4)C(=O)C(c5ccccc5)OC
Canonical SMILES CACTVS 3.385 CO[C@@H](C(=O)N1Cc2[nH]nc(NC(=O)c3ccc(cc3)N4CCN(C)CC4)c2C1)c5ccccc5
Canonical SMILES OpenEye OEToolkits 1.7.6 CN1CCN(CC1)c2ccc(cc2)C(=O)Nc3c4c([nH]n3)CN(C4)C(=O)[C@@H](c5ccccc5)OC

IUPAC InChI

InChI=1S/C26H30N6O3/c1-30-12-14-31(15-13-30)20-10-8-19(9-11-20)25(33)27-24-21-16-32(17-22(21)28-29-24)26(34)23(35-2)18-6-4-3-5-7-18/h3-11,23H,12-17H2,1-2H3,(H2,27,28,29,33)/t23-/m1/s1

IUPAC InChI key

XKFTZKGMDDZMJI-HSZRJFAPSA-N
627

wwPDB Information

Atom count

65 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2006-09-08

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



627 : Atoms of Molecule

Total Number of Atoms: 65
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C10 N Y N 0 -5.573 1.666 0.236
2 C11 C C11 N Y N 0 -4.658 -0.554 0.477
3 C12 C C12 N Y N 0 -3.394 -0.062 0.245
4 C13 C C13 N Y N 0 2.698 1.605 -0.754
5 C14 C C14 N Y N 0 1.681 0.758 -0.494
6 C15 C C15 N N N 0 2.223 -0.64 -0.335
7 C16 C C16 N N N 0 3.994 0.834 -0.787
8 C18 C C18 N N N 0 -6.992 -1.645 0.94
9 C19 C C19 N N N 0 -8.4 -2.143 1.272
10 C20 C C20 R N N 0 6.002 -1.377 -0.784
11 C21 C C21 N N N 0 -9.345 -0.359 -0.064
12 C22 C C22 N N N 0 -7.937 0.138 -0.396
13 C23 C C23 N N N 0 -8.929 -2.527 -1.06
14 C24 C C24 N Y N 0 -5.753 0.306 0.476
15 C25 C C25 N N N 0 4.548 -1.6 -0.456
16 C27 C C27 N Y N 0 6.642 -0.559 0.308
17 C28 C C28 N Y N 0 6.914 0.78 0.1
18 C29 C C29 N Y N 0 6.953 -1.147 1.52
19 C3 C C3 N Y N 0 0.49 1.507 -0.471
20 C31 C C31 N Y N 0 7.497 1.531 1.103
21 C33 C C33 N Y N 0 7.536 -0.396 2.523
22 C35 C C35 N Y N 0 7.807 0.944 2.315
23 C36 C C36 N N N 0 7.767 -2.641 -1.798
24 C6 C C6 N N N 0 -1.856 1.834 -0.24
25 C7 C C7 N Y N 0 -3.21 1.303 0.0090
26 C9 C C9 N Y N 0 -4.312 2.164 0.0040
27 H10 H H10 N N N 0 -6.425 2.33 0.232
28 H11 H H11 N N N 0 -4.801 -1.609 0.659
29 H12 H H12 N N N 0 -2.546 -0.73 0.245
30 H15 H H15 N N N 0 1.783 -1.296 -1.086
31 H151 H H151 N N N 0 1.995 -1.014 0.664
32 H16 H H16 N N N 0 4.669 1.212 -0.019
33 H161 H H161 N N N 0 4.457 0.93 -1.769
34 H181 H H181 N N N 0 -6.631 -2.146 0.041
35 H182 H H182 N N N 0 -6.323 -1.865 1.772
36 H191 H H191 N N N 0 -8.38 -3.224 1.413
37 H192 H H192 N N N 0 -8.75 -1.663 2.186
38 H20 H H20 N N N 0 6.083 -0.844 -1.731
39 H211 H H211 N N N 0 -10.014 -0.139 -0.896
40 H212 H H212 N N N 0 -9.705 0.141 0.835
41 H221 H H221 N N N 0 -7.957 1.219 -0.537
42 H222 H H222 N N N 0 -7.587 -0.342 -1.31
43 H231 H H231 N N N 0 -8.975 -3.601 -0.881
44 H232 H H232 N N N 0 -9.617 -2.263 -1.863
45 H233 H H233 N N N 0 -7.915 -2.249 -1.345
46 H28 H H28 N N N 0 6.672 1.24 -0.847
47 H29 H H29 N N N 0 6.74 -2.193 1.683
48 H31 H H31 N N N 0 7.71 2.578 0.94
49 H33 H H33 N N N 0 7.778 -0.855 3.47
50 H35 H H35 N N N 0 8.263 1.53 3.099
51 H361 H H361 N N N 0 8.217 -3.634 -1.819
52 H362 H H362 N N N 0 7.414 -2.381 -2.796
53 H363 H H363 N N N 0 8.509 -1.912 -1.474
54 H9 H H9 N N N 0 -4.173 3.219 -0.182
55 HN2 H HN2 N N N 0 2.681 3.655 -1.082
56 HN5 H HN5 N N N 0 -0.922 0.056 -0.067
57 N1 N N1 N N N 0 3.677 -0.574 -0.521
58 N17 N N17 N N N 0 -7.029 -0.194 0.711
59 N2 N N2 N Y N 0 2.18 2.846 -0.891
60 N20 N N20 N N N 0 -9.308 -1.811 0.165
61 N4 N N4 N Y N 0 0.795 2.76 -0.709
62 N5 N N5 N N N 0 -0.795 1.003 -0.234
63 O26 O O26 N N N 0 4.161 -2.704 -0.134
64 O34 O O34 N N N 0 6.666 -2.638 -0.887
65 O8 O O8 N N N 0 -1.698 3.021 -0.45



627 : Chemical Bonds

Total Number of Bonds: 69
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C15 N C sing 1.47 N N
2 N1 C16 N C sing 1.47 N N
3 N1 C25 N C sing 1.35 N N
4 N2 N4 N N sing 1.4 N Y
5 N2 HN2 N H sing 0.97 N N
6 N2 C13 N C sing 1.35 N Y
7 C3 N4 C N doub 1.31 N Y
8 C3 N5 C N sing 1.4 N N
9 C3 C14 C C sing 1.41 N Y
10 N5 C6 N C sing 1.35 N N
11 N5 HN5 N H sing 0.97 N N
12 C6 C7 C C sing 1.48 N N
13 C6 O8 C O doub 1.22 N N
14 C7 C9 C C sing 1.4 N Y
15 C7 C12 C C doub 1.4 N Y
16 C9 C10 C C doub 1.38 N Y
17 C9 H9 C H sing 1.08 N N
18 C10 C24 C C sing 1.39 N Y
19 C10 H10 C H sing 1.08 N N
20 C11 C12 C C sing 1.38 N Y
21 C11 C24 C C doub 1.39 N Y
22 C11 H11 C H sing 1.08 N N
23 C12 H12 C H sing 1.08 N N
24 C13 C14 C C doub 1.35 N Y
25 C13 C16 C C sing 1.51 N N
26 C14 C15 C C sing 1.51 N N
27 C15 H15 C H sing 1.09 N N
28 C15 H151 C H sing 1.09 N N
29 C16 H16 C H sing 1.09 N N
30 C16 H161 C H sing 1.09 N N
31 N17 C18 N C sing 1.47 N N
32 N17 C22 N C sing 1.47 N N
33 N17 C24 N C sing 1.39 N N
34 C18 C19 C C sing 1.53 N N
35 C18 H181 C H sing 1.09 N N
36 C18 H182 C H sing 1.09 N N
37 C19 N20 C N sing 1.47 N N
38 C19 H191 C H sing 1.09 N N
39 C19 H192 C H sing 1.09 N N
40 N20 C21 N C sing 1.47 N N
41 N20 C23 N C sing 1.47 N N
42 C21 C22 C C sing 1.53 N N
43 C21 H211 C H sing 1.09 N N
44 C21 H212 C H sing 1.09 N N
45 C22 H221 C H sing 1.09 N N
46 C22 H222 C H sing 1.09 N N
47 C23 H231 C H sing 1.09 N N
48 C23 H232 C H sing 1.09 N N
49 C23 H233 C H sing 1.09 N N
50 C25 O26 C O doub 1.21 N N
51 C25 C20 C C sing 1.51 N N
52 C27 C28 C C sing 1.38 N Y
53 C27 C29 C C doub 1.38 N Y
54 C27 C20 C C sing 1.51 N N
55 C28 C31 C C doub 1.38 N Y
56 C28 H28 C H sing 1.08 N N
57 C29 C33 C C sing 1.38 N Y
58 C29 H29 C H sing 1.08 N N
59 C31 C35 C C sing 1.38 N Y
60 C31 H31 C H sing 1.08 N N
61 C33 C35 C C doub 1.38 N Y
62 C33 H33 C H sing 1.08 N N
63 C20 O34 C O sing 1.43 N N
64 C20 H20 C H sing 1.09 N N
65 C35 H35 C H sing 1.08 N N
66 C36 O34 C O sing 1.43 N N
67 C36 H361 C H sing 1.09 N N
68 C36 H362 C H sing 1.09 N N
69 C36 H363 C H sing 1.09 N N



627 : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
627 2j50 Open in New Window Bound ligand 2 1
627 2v7a Open in New Window Bound ligand 2 1
627 4qo9 Open in New Window Bound ligand 2 1
627 5i9z Open in New Window Bound ligand 1 1