Chemical Components in the PDB

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NUT : Summary

Code

NUT

One-letter code

X

Molecule name

4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one

Synonyms

Nutlin 3a

Systematic names

ProgramVersionName
ACDLabs 12.01 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one
OpenEye OEToolkits 1.7.6 4-[[(4S,5R)-4,5-bis(4-chlorophenyl)-2-(4-methoxy-2-propan-2-yloxy-phenyl)-4,5-dihydroimidazol-1-yl]carbonyl]piperazin-2-one

Formula

C30 H30 Cl2 N4 O4

Formal charge

0

Molecular weight

581.49 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C5NCCN(C(=O)N3C(=NC(c1ccc(Cl)cc1)C3c2ccc(Cl)cc2)c4ccc(OC)cc4OC(C)C)C5
SMILES CACTVS 3.370 COc1ccc(c(OC(C)C)c1)C2=N[CH]([CH](N2C(=O)N3CCNC(=O)C3)c4ccc(Cl)cc4)c5ccc(Cl)cc5
SMILES OpenEye OEToolkits 1.7.6 CC(C)Oc1cc(ccc1C2=NC(C(N2C(=O)N3CCNC(=O)C3)c4ccc(cc4)Cl)c5ccc(cc5)Cl)OC
Canonical SMILES CACTVS 3.370 COc1ccc(c(OC(C)C)c1)C2=N[C@H]([C@H](N2C(=O)N3CCNC(=O)C3)c4ccc(Cl)cc4)c5ccc(Cl)cc5
Canonical SMILES OpenEye OEToolkits 1.7.6 CC(C)Oc1cc(ccc1C2=N[C@H]([C@H](N2C(=O)N3CCNC(=O)C3)c4ccc(cc4)Cl)c5ccc(cc5)Cl)OC

IUPAC InChI

InChI=1S/C30H30Cl2N4O4/c1-18(2)40-25-16-23(39-3)12-13-24(25)29-34-27(19-4-8-21(31)9-5-19)28(20-6-10-22(32)11-7-20)36(29)30(38)35-15-14-33-26(37)17-35/h4-13,16,18,27-28H,14-15,17H2,1-3H3,(H,33,37)/t27-,28+/m0/s1

IUPAC InChI key

BDUHCSBCVGXTJM-WUFINQPMSA-N
NUT

wwPDB Information

Atom count

70 (40 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-10-12

Last modified at

2013-04-19

Status

Released

Obsoleted

Not Assigned



NUT : Atoms of Molecule

Total Number of Atoms: 70
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O3 O O3 N N N 0 2.397 -0.98 -0.849
2 C25 C C25 N N N 0 1.311 -1.194 -0.347
3 N2 N N2 N N N 0 0.673 -2.356 -0.591
4 C29 C C29 N N N 0 -0.534 -2.739 0.158
5 C28 C C28 N N N 0 -0.44 -4.196 0.52
6 O2 O O2 N N N 0 -1.221 -4.641 1.334
7 N3 N N3 N N N 0 0.461 -5.021 -0.014
8 C27 C C27 N N N 0 1.515 -4.612 -0.933
9 C26 C C26 N N N 0 1.151 -3.291 -1.624
10 N1 N N1 N N N 0 0.748 -0.273 0.46
11 C10 C C10 N N N 0 1.231 0.995 0.697
12 C9 C C9 N Y N 0 2.465 1.515 0.075
13 C3 C C3 N Y N 0 2.42 2.663 -0.719
14 C2 C C2 N Y N 0 3.572 3.145 -1.298
15 C5 C C5 N Y N 0 3.687 0.861 0.282
16 O1 O O1 N N N 0 3.74 -0.253 1.056
17 C6 C C6 N N N 0 4.992 -0.939 1.122
18 C8 C C8 N N N 0 5.78 -0.445 2.336
19 C7 C C7 N N N 0 4.743 -2.443 1.252
20 C4 C C4 N Y N 0 4.84 1.354 -0.304
21 C1 C C1 N Y N 0 4.784 2.492 -1.095
22 O O O N N N 0 5.916 2.973 -1.669
23 C C C N N N 0 5.788 4.152 -2.466
24 C18 C C18 R N N 0 -0.493 -0.446 1.234
25 C19 C C19 N Y N 0 -1.661 -0.697 0.316
26 C24 C C24 N Y N 0 -2.639 -1.606 0.675
27 C23 C C23 N Y N 0 -3.711 -1.837 -0.166
28 C22 C C22 N Y N 0 -3.805 -1.159 -1.368
29 CL1 CL CL1 N N N 0 -5.151 -1.448 -2.426
30 C21 C C21 N Y N 0 -2.825 -0.25 -1.728
31 C20 C C20 N Y N 0 -1.757 -0.016 -0.883
32 C11 C C11 S N N 0 -0.651 0.905 1.958
33 N N N N N N 0 0.508 1.691 1.512
34 C12 C C12 N Y N 0 -1.933 1.58 1.54
35 C17 C C17 N Y N 0 -1.994 2.264 0.34
36 C16 C C16 N Y N 0 -3.169 2.883 -0.043
37 C15 C C15 N Y N 0 -4.283 2.818 0.774
38 CL CL CL N N N 0 -5.759 3.595 0.293
39 C14 C C14 N Y N 0 -4.221 2.134 1.975
40 C13 C C13 N Y N 0 -3.047 1.511 2.355
41 H1 H H1 N N N 0 -0.604 -2.141 1.066
42 H2 H H2 N N N 0 -1.416 -2.569 -0.46
43 H3 H H3 N N N 0 0.411 -5.96 0.226
44 H4 H H4 N N N 0 2.445 -4.485 -0.379
45 H5 H H5 N N N 0 1.651 -5.385 -1.689
46 H6 H H6 N N N 0 0.364 -3.462 -2.358
47 H7 H H7 N N N 0 2.031 -2.876 -2.116
48 H9 H H9 N N N 0 1.481 3.173 -0.879
49 H10 H H10 N N N 0 3.536 4.033 -1.911
50 H11 H H11 N N N 0 5.562 -0.742 0.214
51 H12 H H12 N N N 0 5.21 -0.642 3.244
52 H13 H H13 N N N 0 6.736 -0.968 2.386
53 H14 H H14 N N N 0 5.957 0.627 2.243
54 H15 H H15 N N N 0 4.181 -2.795 0.387
55 H16 H H16 N N N 0 5.699 -2.966 1.302
56 H17 H H17 N N N 0 4.173 -2.64 2.16
57 H18 H H18 N N N 0 5.783 0.853 -0.146
58 H19 H H19 N N N 0 5.402 4.966 -1.853
59 H20 H H20 N N N 0 6.765 4.429 -2.864
60 H21 H H21 N N N 0 5.101 3.961 -3.29
61 H22 H H22 N N N 0 -0.387 -1.259 1.952
62 H23 H H23 N N N 0 -2.566 -2.135 1.614
63 H24 H H24 N N N 0 -4.475 -2.547 0.115
64 H25 H H25 N N N 0 -2.898 0.279 -2.666
65 H26 H H26 N N N 0 -0.995 0.697 -1.161
66 H27 H H27 N N N 0 -0.628 0.765 3.038
67 H30 H H30 N N N 0 -1.124 2.314 -0.298
68 H31 H H31 N N N 0 -3.217 3.417 -0.981
69 H32 H H32 N N N 0 -5.09 2.084 2.614
70 H33 H H33 N N N 0 -3.0 0.973 3.29



NUT : Chemical Bonds

Total Number of Bonds: 74
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2 C28 O C doub 1.2126756 N N
2 C28 C29 C C sing 1.504237 N N
3 C28 N3 C N sing 1.3332599 N N
4 C29 N2 C N sing 1.4712372 N N
5 O3 C25 O C doub 1.2153995 N N
6 N3 C27 N C sing 1.4569688 N N
7 C25 N2 C N sing 1.3478961 N N
8 C25 N1 C N sing 1.3477607 N N
9 N2 C26 N C sing 1.4730234 N N
10 C27 C26 C C sing 1.5346068 N N
11 C11 C18 C C sing 1.5408896 N N
12 C11 N C N sing 1.4696915 N N
13 C11 C12 C C sing 1.5079367 N N
14 C3 C2 C C doub 1.3764697 N Y
15 C3 C9 C C sing 1.3965547 N Y
16 N1 C18 N C sing 1.4727818 N N
17 N1 C10 N C sing 1.3774186 N N
18 C2 C1 C C sing 1.3916041 N Y
19 C17 C12 C C doub 1.3825979 N Y
20 C17 C16 C C sing 1.3821993 N Y
21 C18 C19 C C sing 1.506635 N N
22 C10 N C N doub 1.2928147 N N
23 C10 C9 C C sing 1.4764959 N N
24 C9 C5 C C doub 1.401374 N Y
25 C O C O sing 1.4288576 N N
26 C12 C13 C C sing 1.382021 N Y
27 C1 O C O sing 1.3572992 N N
28 C1 C4 C C doub 1.3870332 N Y
29 C16 C15 C C doub 1.3830076 N Y
30 C5 C4 C C sing 1.3841438 N Y
31 C5 O1 C O sing 1.3575275 N N
32 C8 C6 C C sing 1.5293057 N N
33 O1 C6 O C sing 1.4291452 N N
34 C19 C24 C C doub 1.3826228 N Y
35 C19 C20 C C sing 1.3822366 N Y
36 C24 C23 C C sing 1.3819646 N Y
37 C13 C14 C C doub 1.3823187 N Y
38 C15 C14 C C sing 1.3835104 N Y
39 C15 CL C CL sing 1.7359914 N N
40 C6 C7 C C sing 1.5300056 N N
41 C20 C21 C C doub 1.3818122 N Y
42 C23 C22 C C doub 1.3832296 N Y
43 C21 C22 C C sing 1.384298 N Y
44 C22 CL1 C CL sing 1.7362607 N N
45 C29 H1 C H sing 1.0894806 N N
46 C29 H2 C H sing 1.0902972 N N
47 N3 H3 N H sing 0.9704746 N N
48 C27 H4 C H sing 1.0899289 N N
49 C27 H5 C H sing 1.0897527 N N
50 C26 H6 C H sing 1.0896633 N N
51 C26 H7 C H sing 1.0902702 N N
52 C3 H9 C H sing 1.0804726 N N
53 C2 H10 C H sing 1.0796337 N N
54 C6 H11 C H sing 1.0900335 N N
55 C8 H12 C H sing 1.0900335 N N
56 C8 H13 C H sing 1.0908551 N N
57 C8 H14 C H sing 1.090487 N N
58 C7 H15 C H sing 1.0899417 N N
59 C7 H16 C H sing 1.0908551 N N
60 C7 H17 C H sing 1.0900335 N N
61 C4 H18 C H sing 1.0794508 N N
62 C H19 C H sing 1.089661 N N
63 C H20 C H sing 1.0907162 N N
64 C H21 C H sing 1.0896908 N N
65 C18 H22 C H sing 1.0898298 N N
66 C24 H23 C H sing 1.0802273 N N
67 C23 H24 C H sing 1.0801653 N N
68 C21 H25 C H sing 1.0793581 N N
69 C20 H26 C H sing 1.0799524 N N
70 C11 H27 C H sing 1.0892792 N N
71 C17 H30 C H sing 1.0800204 N N
72 C16 H31 C H sing 1.0804185 N N
73 C14 H32 C H sing 1.0798064 N N
74 C13 H33 C H sing 1.0797583 N N



NUT : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
NUT 4hg7 Open in New Window Bound ligand 1 1
NUT 4j3e Open in New Window Bound ligand 1 1