Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

9XH : Summary

Code

9XH

One-letter code

X

Molecule name

(2~{S})-2-azanyl-4-[4-[bis(4-fluorophenyl)methyl]piperazin-1-yl]-1-(1,3-dihydroisoindol-2-yl)butane-1,4-dione

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 (2~{S})-2-azanyl-4-[4-[bis(4-fluorophenyl)methyl]piperazin-1-yl]-1-(1,3-dihydroisoindol-2-yl)butane-1,4-dione

Formula

C29 H30 F2 N4 O2

Formal charge

0

Molecular weight

504.571 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 N[CH](CC(=O)N1CCN(CC1)C(c2ccc(F)cc2)c3ccc(F)cc3)C(=O)N4Cc5ccccc5C4
SMILES OpenEye OEToolkits 2.0.6 c1ccc2c(c1)CN(C2)C(=O)C(CC(=O)N3CCN(CC3)C(c4ccc(cc4)F)c5ccc(cc5)F)N
Canonical SMILES CACTVS 3.385 N[C@@H](CC(=O)N1CCN(CC1)C(c2ccc(F)cc2)c3ccc(F)cc3)C(=O)N4Cc5ccccc5C4
Canonical SMILES OpenEye OEToolkits 2.0.6 c1ccc2c(c1)CN(C2)C(=O)[C@H](CC(=O)N3CCN(CC3)C(c4ccc(cc4)F)c5ccc(cc5)F)N

IUPAC InChI

InChI=1S/C29H30F2N4O2/c30-24-9-5-20(6-10-24)28(21-7-11-25(31)12-8-21)34-15-13-33(14-16-34)27(36)17-26(32)29(37)35-18-22-3-1-2-4-23(22)19-35/h1-12,26,28H,13-19,32H2/t26-/m0/s1

IUPAC InChI key

ZKIQFLSGMMYCGS-SANMLTNESA-N
9XH

wwPDB Information

Atom count

67 (37 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-07-26

Last modified at

2018-02-02

Status

Released

Obsoleted

Not Assigned



9XH : Atoms of Molecule

Total Number of Atoms: 67
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 7.628 2.293 -0.845
2 C2 C C2 N Y N 0 7.541 2.959 -2.052
3 C3 C C3 N Y N 0 6.555 2.619 -2.959
4 C4 C C4 N Y N 0 5.657 1.613 -2.657
5 C5 C C5 N Y N 0 5.744 0.945 -1.448
6 C6 C C6 N Y N 0 6.729 1.285 -0.542
7 C7 C C7 N N N 0 6.596 0.405 0.675
8 C12 C C8 S N N 0 3.816 -2.282 0.923
9 N13 N N1 N N N 0 3.805 -3.506 1.735
10 C15 C C9 N N N 0 1.348 -2.289 0.678
11 C18 C C10 N N N 0 -1.064 -2.549 0.319
12 C19 C C11 N N N 0 -1.9 -1.642 -0.589
13 C21 C C12 N N N 0 -1.001 0.357 0.449
14 C23 C C13 N N N 0 -3.161 0.425 -0.643
15 C24 C C14 N Y N 0 -4.395 -0.382 -0.955
16 C27 C C15 N Y N 0 -6.659 -1.863 -1.527
17 C30 C C16 N Y N 0 -4.995 -0.275 -2.196
18 C31 C C17 N Y N 0 -3.545 1.638 0.165
19 C32 C C18 N Y N 0 -3.763 1.52 1.525
20 C33 C C19 N Y N 0 -4.115 2.631 2.267
21 C34 C C20 N Y N 0 -4.248 3.863 1.649
22 C36 C C21 N Y N 0 -4.029 3.979 0.287
23 C37 C C22 N Y N 0 -3.672 2.868 -0.453
24 N8 N N2 N N N 0 5.458 -0.493 0.454
25 C9 C C23 N N N 0 4.913 -0.172 -0.868
26 C10 C C24 N N N 0 5.004 -1.437 1.302
27 O11 O O1 N N N 0 5.552 -1.607 2.371
28 C14 C C25 N N N 0 2.529 -1.493 1.172
29 O16 O O2 N N N 0 1.519 -3.381 0.177
30 N17 N N3 N N N 0 0.102 -1.789 0.794
31 N20 N N4 N N N 0 -2.219 -0.398 0.126
32 C22 C C26 N N N 0 -0.128 -0.468 1.4
33 C25 C C27 N Y N 0 -4.922 -1.234 -0.002
34 C26 C C28 N Y N 0 -6.054 -1.974 -0.287
35 F28 F F1 N N N 0 -7.765 -2.587 -1.807
36 C29 C C29 N Y N 0 -6.127 -1.014 -2.483
37 F35 F F2 N N N 0 -4.593 4.95 2.373
38 H1 H H1 N N N 0 8.402 2.555 -0.139
39 H2 H H2 N N N 0 8.243 3.745 -2.287
40 H3 H H3 N N N 0 6.486 3.139 -3.903
41 H4 H H4 N N N 0 4.886 1.348 -3.366
42 H5 H H5 N N N 0 7.507 -0.179 0.81
43 H6 H H6 N N N 0 3.881 -2.548 -0.132
44 H7 H H7 N N N 0 3.745 -3.286 2.719
45 H8 H H8 N N N 0 3.054 -4.119 1.456
46 H11 H H11 N N N 0 -1.665 -2.868 1.171
47 H12 H H12 N N N 0 -0.732 -3.423 -0.242
48 H13 H H13 N N N 0 -1.334 -1.408 -1.49
49 H14 H H14 N N N 0 -2.824 -2.151 -0.862
50 H15 H H15 N N N 0 -0.447 0.563 -0.467
51 H16 H H16 N N N 0 -1.273 1.298 0.928
52 H17 H H17 N N N 0 -2.69 0.743 -1.574
53 H18 H H18 N N N 0 -4.579 0.387 -2.941
54 H19 H H19 N N N 0 -3.659 0.559 2.007
55 H20 H H20 N N N 0 -4.286 2.539 3.33
56 H21 H H21 N N N 0 -4.133 4.939 -0.197
57 H22 H H22 N N N 0 -3.498 2.959 -1.515
58 H23 H H23 N N N 0 3.876 0.15 -0.773
59 H24 H H24 N N N 0 2.419 -1.305 2.24
60 H25 H H25 N N N 0 2.575 -0.544 0.638
61 H29 H H29 N N N 0 0.826 0.036 1.552
62 H30 H H30 N N N 0 -0.639 -0.588 2.355
63 H31 H H31 N N N 0 -4.45 -1.32 0.965
64 H32 H H32 N N N 0 -6.468 -2.636 0.459
65 H33 H H33 N N N 0 -6.598 -0.927 -3.451
66 H9 H H9 N N N 0 4.97 -1.048 -1.514
67 H10 H H10 N N N 0 6.416 1.019 1.557



9XH : Chemical Bonds

Total Number of Bonds: 71
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 F28 C27 F C sing 1.35 N N
2 C3 C2 C C sing 1.38 N Y
3 C3 C4 C C doub 1.38 N Y
4 C27 C26 C C doub 1.38 N Y
5 C27 C29 C C sing 1.38 N Y
6 C26 C25 C C sing 1.38 N Y
7 C2 C1 C C doub 1.38 N Y
8 C4 C5 C C sing 1.38 N Y
9 C29 C30 C C doub 1.38 N Y
10 C33 C32 C C doub 1.38 N Y
11 C33 C34 C C sing 1.38 N Y
12 C32 C31 C C sing 1.38 N Y
13 C25 C24 C C doub 1.38 N Y
14 O16 C15 O C doub 1.21 N N
15 C30 C24 C C sing 1.38 N Y
16 C24 C23 C C sing 1.51 N N
17 C1 C6 C C sing 1.38 N Y
18 C5 C6 C C doub 1.38 N Y
19 C5 C9 C C sing 1.51 N N
20 F35 C34 F C sing 1.35 N N
21 C34 C36 C C doub 1.38 N Y
22 C6 C7 C C sing 1.51 N N
23 C31 C23 C C sing 1.51 N N
24 C31 C37 C C doub 1.38 N Y
25 C23 N20 C N sing 1.47 N N
26 C22 N17 C N sing 1.47 N N
27 C22 C21 C C sing 1.53 N N
28 C9 N8 C N sing 1.47 N N
29 N17 C15 N C sing 1.35 N N
30 N17 C18 N C sing 1.47 N N
31 C15 C14 C C sing 1.51 N N
32 C18 C19 C C sing 1.53 N N
33 C7 N8 C N sing 1.47 N N
34 N8 C10 N C sing 1.35 N N
35 C36 C37 C C sing 1.38 N Y
36 C12 C14 C C sing 1.53 N N
37 C12 C10 C C sing 1.51 N N
38 C12 N13 C N sing 1.47 N N
39 N20 C21 N C sing 1.47 N N
40 N20 C19 N C sing 1.47 N N
41 C10 O11 C O doub 1.21 N N
42 C1 H1 C H sing 1.08 N N
43 C2 H2 C H sing 1.08 N N
44 C3 H3 C H sing 1.08 N N
45 C4 H4 C H sing 1.08 N N
46 C7 H5 C H sing 1.09 N N
47 C12 H6 C H sing 1.09 N N
48 N13 H7 N H sing 1.01 N N
49 N13 H8 N H sing 1.01 N N
50 C18 H11 C H sing 1.09 N N
51 C18 H12 C H sing 1.09 N N
52 C19 H13 C H sing 1.09 N N
53 C19 H14 C H sing 1.09 N N
54 C21 H15 C H sing 1.09 N N
55 C21 H16 C H sing 1.09 N N
56 C23 H17 C H sing 1.09 N N
57 C30 H18 C H sing 1.08 N N
58 C32 H19 C H sing 1.08 N N
59 C33 H20 C H sing 1.08 N N
60 C36 H21 C H sing 1.08 N N
61 C37 H22 C H sing 1.08 N N
62 C9 H23 C H sing 1.09 N N
63 C14 H24 C H sing 1.09 N N
64 C14 H25 C H sing 1.09 N N
65 C22 H29 C H sing 1.09 N N
66 C22 H30 C H sing 1.09 N N
67 C25 H31 C H sing 1.08 N N
68 C26 H32 C H sing 1.08 N N
69 C29 H33 C H sing 1.08 N N
70 C9 H9 C H sing 1.09 N N
71 C7 H10 C H sing 1.09 N N



9XH : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
9XH 6eor Open in New Window Bound ligand 4 1
9XH 6trx Open in New Window Bound ligand 3 1