Chemical Components in the PDB

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N53 : Summary

Code

N53

One-letter code

X

Molecule name

N-[6,6-dimethyl-5-[(2S)-4-methyl-2-(phenylmethyl)piperazin-1-yl]carbonyl-2,4-dihydropyrrolo[3,4-c]pyrazol-3-yl]-3-phenoxy-benzamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-(5-{[(2S)-2-benzyl-4-methylpiperazin-1-yl]carbonyl}-6,6-dimethyl-2,4,5,6-tetrahydropyrrolo[3,4-c]pyrazol-3-yl)-3-phenoxybenzamide
OpenEye OEToolkits 1.9.2 N-[6,6-dimethyl-5-[(2S)-4-methyl-2-(phenylmethyl)piperazin-1-yl]carbonyl-2,4-dihydropyrrolo[3,4-c]pyrazol-3-yl]-3-phenoxy-benzamide

Formula

C33 H36 N6 O3

Formal charge

0

Molecular weight

564.677 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(c2cccc(Oc1ccccc1)c2)Nc3c6c(nn3)C(N(C(=O)N5C(Cc4ccccc4)CN(C)CC5)C6)(C)C
SMILES CACTVS 3.385 CN1CCN([CH](C1)Cc2ccccc2)C(=O)N3Cc4c([nH]nc4C3(C)C)NC(=O)c5cccc(Oc6ccccc6)c5
SMILES OpenEye OEToolkits 1.9.2 CC1(c2c(c([nH]n2)NC(=O)c3cccc(c3)Oc4ccccc4)CN1C(=O)N5CCN(CC5Cc6ccccc6)C)C
Canonical SMILES CACTVS 3.385 CN1CCN([C@H](C1)Cc2ccccc2)C(=O)N3Cc4c([nH]nc4C3(C)C)NC(=O)c5cccc(Oc6ccccc6)c5
Canonical SMILES OpenEye OEToolkits 1.9.2 CC1(c2c(c([nH]n2)NC(=O)c3cccc(c3)Oc4ccccc4)CN1C(=O)N5CCN(C[C@@H]5Cc6ccccc6)C)C

IUPAC InChI

InChI=1S/C33H36N6O3/c1-33(2)29-28(22-39(33)32(41)38-18-17-37(3)21-25(38)19-23-11-6-4-7-12-23)30(36-35-29)34-31(40)24-13-10-16-27(20-24)42-26-14-8-5-9-15-26/h4-16,20,25H,17-19,21-22H2,1-3H3,(H2,34,35,36,40)/t25-/m0/s1

IUPAC InChI key

VGRHRLOVUZTBHT-VWLOTQADSA-N
N53

wwPDB Information

Atom count

78 (42 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-04-04

Last modified at

2014-09-05

Status

Released

Obsoleted

Not Assigned



N53 : Atoms of Molecule

Total Number of Atoms: 78
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 -8.578 0.775 0.179
2 C2 C C2 N Y N 0 -8.435 -0.057 1.281
3 C3 C C3 N Y N 0 -9.01 -1.313 1.276
4 C4 C C4 N Y N 0 -9.729 -1.742 0.175
5 C5 C C5 N Y N 0 -9.873 -0.915 -0.924
6 C6 C C6 N Y N 0 -9.3 0.342 -0.925
7 C7 C C7 N Y N 0 -4.502 1.045 0.077
8 C8 C C8 N Y N 0 -5.894 0.952 0.072
9 C9 C C9 N Y N 0 -6.661 2.099 0.189
10 C10 C C10 N Y N 0 -6.045 3.337 0.311
11 C11 C C11 N Y N 0 -4.666 3.431 0.317
12 C12 C C12 N Y N 0 -3.892 2.294 0.201
13 C13 C C13 N Y N 0 7.594 -0.121 0.279
14 C14 C C14 N Y N 0 8.184 -0.434 1.489
15 C15 C C15 N Y N 0 9.502 -0.09 1.725
16 C16 C C16 N Y N 0 10.23 0.568 0.751
17 C17 C C17 N Y N 0 9.64 0.881 -0.459
18 C18 C C18 N Y N 0 8.322 0.538 -0.695
19 N19 N N19 N N N 0 3.844 0.299 0.143
20 C20 C C20 S N N 0 5.248 0.677 0.369
21 C21 C C21 N N N 0 5.581 1.87 -0.533
22 N22 N N22 N N N 0 4.604 2.943 -0.301
23 C23 C C23 N N N 0 3.248 2.518 -0.672
24 C24 C C24 N N N 0 2.819 1.351 0.223
25 C25 C C25 N Y N 0 0.184 -2.626 -0.282
26 C26 C C26 N N N 0 1.053 -0.44 -0.089
27 N27 N N27 N N N 0 2.209 -1.339 -0.166
28 C28 C C28 N N N 0 1.69 -2.703 -0.294
29 N29 N N29 N Y N 0 -0.903 -3.355 -0.349
30 N30 N N30 N Y N 0 -2.013 -2.505 -0.266
31 C31 C C31 N Y N 0 -1.554 -1.233 -0.147
32 C32 C C32 N N N 0 2.167 -3.318 -1.61
33 C33 C C33 N N N 0 2.174 -3.554 0.882
34 C34 C C34 N N N 0 3.507 -0.976 -0.135
35 O35 O O35 N N N 0 4.373 -1.799 -0.358
36 C36 C C36 N N N 0 4.987 4.167 -1.016
37 C37 C C37 N N N 0 6.159 -0.502 0.019
38 N38 N N38 N N N 0 -2.332 -0.082 -0.035
39 C39 C C39 N N N 0 -3.677 -0.175 -0.041
40 O40 O O40 N N N 0 -4.21 -1.263 -0.143
41 O41 O O41 N N N 0 -8.018 2.012 0.183
42 C42 C C42 N Y N 0 -0.192 -1.287 -0.162
43 H2 H H2 N N N 0 -7.874 0.277 2.141
44 H6 H H6 N N N 0 -9.413 0.987 -1.783
45 H3 H H3 N N N 0 -8.899 -1.96 2.133
46 H4 H H4 N N N 0 -10.177 -2.724 0.173
47 H5 H H5 N N N 0 -10.434 -1.252 -1.783
48 H8 H H8 N N N 0 -6.372 -0.012 -0.024
49 H12 H H12 N N N 0 -2.815 2.371 0.206
50 H10 H H10 N N N 0 -6.646 4.23 0.402
51 H11 H H11 N N N 0 -4.193 4.397 0.413
52 H14 H H14 N N N 0 7.616 -0.948 2.25
53 H18 H H18 N N N 0 7.861 0.782 -1.64
54 H371 H H371 N N N 0 6.036 -0.757 -1.033
55 H372 H H372 N N N 0 5.894 -1.361 0.635
56 H15 H H15 N N N 0 9.963 -0.335 2.671
57 H16 H H16 N N N 0 11.259 0.837 0.936
58 H17 H H17 N N N 0 10.208 1.395 -1.22
59 H20 H H20 N N N 0 5.389 0.955 1.413
60 H241 H H241 N N N 0 1.863 0.957 -0.122
61 H242 H H242 N N N 0 2.727 1.694 1.254
62 H211 H H211 N N N 0 6.582 2.233 -0.299
63 H212 H H212 N N N 0 5.54 1.561 -1.577
64 H231 H H231 N N N 0 2.557 3.35 -0.54
65 H232 H H232 N N N 0 3.24 2.199 -1.714
66 H361 H H361 N N N 0 5.034 3.963 -2.086
67 H362 H H362 N N N 0 4.247 4.945 -0.827
68 H363 H H363 N N N 0 5.964 4.502 -0.667
69 H261 H H261 N N N 0 1.068 0.102 0.856
70 H262 H H262 N N N 0 1.077 0.265 -0.92
71 H321 H H321 N N N 0 1.81 -2.714 -2.444
72 H322 H H322 N N N 0 3.257 -3.348 -1.624
73 H323 H H323 N N N 0 1.775 -4.331 -1.702
74 H331 H H331 N N N 0 1.85 -4.586 0.742
75 H332 H H332 N N N 0 3.262 -3.519 0.933
76 H333 H H333 N N N 0 1.753 -3.165 1.81
77 H30 H H30 N N N 0 -2.944 -2.777 -0.29
78 H38 H H38 N N N 0 -1.906 0.785 0.046



N53 : Chemical Bonds

Total Number of Bonds: 83
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.39 N Y
2 C1 C6 C C doub 1.39 N Y
3 C1 O41 C O sing 1.36 N N
4 C2 C3 C C doub 1.38 N Y
5 C3 C4 C C sing 1.38 N Y
6 C4 C5 C C doub 1.38 N Y
7 C5 C6 C C sing 1.38 N Y
8 C7 C8 C C sing 1.4 N Y
9 C7 C12 C C doub 1.4 N Y
10 C7 C39 C C sing 1.48 N N
11 C8 C9 C C doub 1.38 N Y
12 C9 C10 C C sing 1.39 N Y
13 C9 O41 C O sing 1.36 N N
14 C10 C11 C C doub 1.38 N Y
15 C11 C12 C C sing 1.38 N Y
16 C13 C14 C C sing 1.38 N Y
17 C13 C18 C C doub 1.38 N Y
18 C13 C37 C C sing 1.51 N N
19 C14 C15 C C doub 1.38 N Y
20 C15 C16 C C sing 1.38 N Y
21 C16 C17 C C doub 1.38 N Y
22 C17 C18 C C sing 1.38 N Y
23 N19 C20 N C sing 1.47 N N
24 N19 C24 N C sing 1.47 N N
25 N19 C34 N C sing 1.35 N N
26 C20 C21 C C sing 1.53 N N
27 C20 C37 C C sing 1.53 N N
28 C21 N22 C N sing 1.47 N N
29 N22 C23 N C sing 1.47 N N
30 N22 C36 N C sing 1.47 N N
31 C23 C24 C C sing 1.53 N N
32 C25 C28 C C sing 1.51 N N
33 C25 N29 C N doub 1.31 N Y
34 C25 C42 C C sing 1.4 N Y
35 C26 N27 C N sing 1.47 N N
36 C26 C42 C C sing 1.51 N N
37 N27 C28 N C sing 1.47 N N
38 N27 C34 N C sing 1.35 N N
39 C28 C32 C C sing 1.53 N N
40 C28 C33 C C sing 1.53 N N
41 N29 N30 N N sing 1.4 N Y
42 N30 C31 N C sing 1.36 N Y
43 C31 N38 C N sing 1.39 N N
44 C31 C42 C C doub 1.36 N Y
45 C34 O35 C O doub 1.22 N N
46 N38 C39 N C sing 1.35 N N
47 C39 O40 C O doub 1.22 N N
48 C2 H2 C H sing 1.08 N N
49 C6 H6 C H sing 1.08 N N
50 C3 H3 C H sing 1.08 N N
51 C4 H4 C H sing 1.08 N N
52 C5 H5 C H sing 1.08 N N
53 C8 H8 C H sing 1.08 N N
54 C12 H12 C H sing 1.08 N N
55 C10 H10 C H sing 1.08 N N
56 C11 H11 C H sing 1.08 N N
57 C14 H14 C H sing 1.08 N N
58 C18 H18 C H sing 1.08 N N
59 C37 H371 C H sing 1.09 N N
60 C37 H372 C H sing 1.09 N N
61 C15 H15 C H sing 1.08 N N
62 C16 H16 C H sing 1.08 N N
63 C17 H17 C H sing 1.08 N N
64 C20 H20 C H sing 1.09 N N
65 C24 H241 C H sing 1.09 N N
66 C24 H242 C H sing 1.09 N N
67 C21 H211 C H sing 1.09 N N
68 C21 H212 C H sing 1.09 N N
69 C23 H231 C H sing 1.09 N N
70 C23 H232 C H sing 1.09 N N
71 C36 H361 C H sing 1.09 N N
72 C36 H362 C H sing 1.09 N N
73 C36 H363 C H sing 1.09 N N
74 C26 H261 C H sing 1.09 N N
75 C26 H262 C H sing 1.09 N N
76 C32 H321 C H sing 1.09 N N
77 C32 H322 C H sing 1.09 N N
78 C32 H323 C H sing 1.09 N N
79 C33 H331 C H sing 1.09 N N
80 C33 H332 C H sing 1.09 N N
81 C33 H333 C H sing 1.09 N N
82 N30 H30 N H sing 0.97 N N
83 N38 H38 N H sing 0.97 N N



N53 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
N53 4app Open in New Window Bound ligand 1 1