Chemical Components in the PDB

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KLN : Summary

Code

KLN

One-letter code

X

Molecule name

1-ACETYL-4-(4-{[(2S,4R)-2-(2,4-DICHLOROPHENYL)-2-(1H-IMIDAZOL-1-YLMETHYL)-1,3-DIOXOLAN-4-YL]METHOXY}PHENYL)PIPERAZINE

Systematic names

ProgramVersionName
ACDLabs 10.04 1-acetyl-4-(4-{[(2S,4R)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine
OpenEye OEToolkits 1.5.0 1-[4-[4-[[(2S,4R)-2-(2,4-dichlorophenyl)-2-(imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy]phenyl]piperazin-1-yl]ethanone

Formula

C26 H28 Cl2 N4 O4

Formal charge

0

Molecular weight

531.431 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(N5CCN(c4ccc(OCC1OC(OC1)(c2ccc(Cl)cc2Cl)Cn3cncc3)cc4)CC5)C
SMILES CACTVS 3.341 CC(=O)N1CCN(CC1)c2ccc(OC[CH]3CO[C](Cn4ccnc4)(O3)c5ccc(Cl)cc5Cl)cc2
SMILES OpenEye OEToolkits 1.5.0 CC(=O)N1CCN(CC1)c2ccc(cc2)OCC3COC(O3)(Cn4ccnc4)c5ccc(cc5Cl)Cl
Canonical SMILES CACTVS 3.341 CC(=O)N1CCN(CC1)c2ccc(OC[C@@H]3CO[C@](Cn4ccnc4)(O3)c5ccc(Cl)cc5Cl)cc2
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(=O)N1CCN(CC1)c2ccc(cc2)OC[C@@H]3CO[C@@](O3)(Cn4ccnc4)c5ccc(cc5Cl)Cl

IUPAC InChI

InChI=1S/C26H28Cl2N4O4/c1-19(33)31-10-12-32(13-11-31)21-3-5-22(6-4-21)34-15-23-16-35-26(36-23,17-30-9-8-29-18-30)24-7-2-20(27)14-25(24)28/h2-9,14,18,23H,10-13,15-17H2,1H3/t23-,26-/m1/s1

IUPAC InChI key

XMAYWYJOQHXEEK-ZEQKJWHPSA-N
KLN

wwPDB Information

Atom count

64 (36 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2007-05-15

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



KLN : Atoms of Molecule

Total Number of Atoms: 64
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 -2.284 -4.006 -0.097
2 C10 C C10 N Y N 0 -6.213 1.749 0.161
3 C11 C C11 N Y N 0 -6.954 1.512 -0.983
4 C12 C C12 N Y N 0 -6.607 0.472 -1.827
5 C13 C C13 N Y N 0 -5.517 -0.325 -1.531
6 C14 C C14 N N N 0 -0.343 -0.412 1.293
7 C15 C C15 N Y N 0 1.555 0.916 0.754
8 C16 C C16 N Y N 0 2.148 2.096 0.331
9 C17 C C17 N Y N 0 3.523 2.181 0.232
10 C18 C C18 N Y N 0 4.312 1.084 0.557
11 C19 C C19 N Y N 0 3.716 -0.097 0.98
12 C2 C C2 N Y N 0 -0.248 -3.672 -0.726
13 C20 C C20 N Y N 0 2.341 -0.178 1.083
14 C21 C C21 N N N 0 6.339 -0.097 0.846
15 C22 C C22 N N N 0 7.859 0.091 0.898
16 C23 C C23 N N N 0 7.622 1.833 -0.914
17 C24 C C24 N N N 0 6.112 1.576 -0.895
18 C25 C C25 N N N 0 9.315 0.065 -1.074
19 C26 C C26 N N N 0 10.082 -1.08 -0.465
20 C3 C C3 N Y N 0 -0.981 -2.661 -1.23
21 C4 C C4 N N N 0 -3.43 -2.03 -1.146
22 C5 C C5 S N N 0 -3.596 -0.965 -0.061
23 C6 C C6 R N N 0 -1.869 -0.315 1.339
24 C7 C C7 N N N 0 -2.489 -1.651 1.818
25 C8 C C8 N Y N 0 -4.78 -0.091 -0.386
26 C9 C C9 N Y N 0 -5.126 0.948 0.46
27 CL1 CL CL1 N N N 0 -8.318 2.517 -1.358
28 CL2 CL CL2 N N N 0 -4.196 1.245 1.895
29 H1 H H1 N N N 0 -3.154 -4.448 0.366
30 H10 H H10 N N N 0 -6.483 2.56 0.821
31 H12 H H12 N N N 0 -7.185 0.286 -2.72
32 H13 H H13 N N N 0 -5.244 -1.133 -2.194
33 H141 H 1H14 N N N 0 0.036 -0.641 2.289
34 H142 H 2H14 N N N 0 -0.05 -1.203 0.602
35 H16 H H16 N N N 0 1.535 2.948 0.078
36 H17 H H17 N N N 0 3.986 3.099 -0.097
37 H19 H H19 N N N 0 4.328 -0.95 1.233
38 H2 H H2 N N N 0 0.816 -3.809 -0.854
39 H20 H H20 N N N 0 1.878 -1.095 1.417
40 H211 H 1H21 N N N 0 5.976 -0.399 1.829
41 H212 H 2H21 N N N 0 6.092 -0.867 0.115
42 H221 H 1H22 N N N 0 8.115 0.784 1.7
43 H222 H 2H22 N N N 0 8.341 -0.87 1.074
44 H231 H 1H23 N N N 0 7.856 2.693 -0.287
45 H232 H 2H23 N N N 0 7.948 2.022 -1.937
46 H241 H 1H24 N N N 0 5.869 0.783 -1.602
47 H242 H 2H24 N N N 0 5.584 2.487 -1.175
48 H261 H 1H26 N N N 0 9.655 -2.024 -0.805
49 H262 H 2H26 N N N 0 11.126 -1.022 -0.772
50 H263 H 3H26 N N N 0 10.019 -1.023 0.621
51 H3 H H3 N N N 0 -0.62 -1.842 -1.833
52 H4C1 H 1H4C N N N 0 -3.274 -1.546 -2.11
53 H4C2 H 2H4C N N N 0 -4.327 -2.647 -1.19
54 H6 H H6 N N N 0 -2.185 0.508 1.98
55 H7C1 H 1H7C N N N 0 -1.919 -2.502 1.444
56 H7C2 H 2H7C N N N 0 -2.562 -1.68 2.905
57 N1 N N1 N Y N 0 -2.273 -2.873 -0.831
58 N2 N N2 N Y N 0 -1.069 -4.479 -0.039
59 N3 N N3 N N N 0 5.705 1.169 0.457
60 N4 N N4 N N N 0 8.306 0.64 -0.391
61 O1 O O1 N N N 0 -2.41 -0.162 0.011
62 O2 O O2 N N N 0 -3.803 -1.6 1.212
63 O3 O O3 N N N 0 0.201 0.833 0.851
64 O4 O O4 N N N 0 9.607 0.47 -2.18



KLN : Chemical Bonds

Total Number of Bonds: 68
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C1 N C sing 1.35 N Y
2 C1 N2 C N doub 1.31 N Y
3 N2 C2 N C sing 1.34 N Y
4 N1 C3 N C sing 1.37 N Y
5 C2 C3 C C doub 1.35 N Y
6 N1 C4 N C sing 1.47 N N
7 C4 C5 C C sing 1.53 N N
8 C5 O1 C O sing 1.43 N N
9 O1 C6 O C sing 1.44 N N
10 C6 C7 C C sing 1.55 N N
11 C5 O2 C O sing 1.44 N N
12 C7 O2 C O sing 1.45 N N
13 C5 C8 C C sing 1.51 N N
14 C8 C9 C C sing 1.38 N Y
15 C9 C10 C C doub 1.38 N Y
16 C10 C11 C C sing 1.38 N Y
17 C11 C12 C C doub 1.38 N Y
18 C8 C13 C C doub 1.38 N Y
19 C12 C13 C C sing 1.38 N Y
20 C11 CL1 C CL sing 1.74 N N
21 C6 C14 C C sing 1.53 N N
22 C14 O3 C O sing 1.43 N N
23 O3 C15 O C sing 1.36 N N
24 C15 C16 C C doub 1.39 N Y
25 C17 C16 C C sing 1.38 N Y
26 C18 C17 C C doub 1.39 N Y
27 C19 C18 C C sing 1.39 N Y
28 C20 C19 C C doub 1.38 N Y
29 C15 C20 C C sing 1.39 N Y
30 C18 N3 C N sing 1.4 N N
31 N3 C21 N C sing 1.47 N N
32 C21 C22 C C sing 1.53 N N
33 C22 N4 C N sing 1.47 N N
34 N4 C23 N C sing 1.47 N N
35 N3 C24 N C sing 1.47 N N
36 C23 C24 C C sing 1.53 N N
37 N4 C25 N C sing 1.35 N N
38 C25 O4 C O doub 1.21 N N
39 C25 C26 C C sing 1.51 N N
40 C9 CL2 C CL sing 1.74 N N
41 C1 H1 C H sing 1.08 N N
42 C3 H3 C H sing 1.08 N N
43 C4 H4C1 C H sing 1.09 N N
44 C4 H4C2 C H sing 1.09 N N
45 C2 H2 C H sing 1.08 N N
46 C6 H6 C H sing 1.09 N N
47 C7 H7C1 C H sing 1.09 N N
48 C7 H7C2 C H sing 1.09 N N
49 C14 H141 C H sing 1.09 N N
50 C14 H142 C H sing 1.09 N N
51 C13 H13 C H sing 1.08 N N
52 C10 H10 C H sing 1.08 N N
53 C12 H12 C H sing 1.08 N N
54 C20 H20 C H sing 1.08 N N
55 C16 H16 C H sing 1.08 N N
56 C19 H19 C H sing 1.08 N N
57 C17 H17 C H sing 1.08 N N
58 C21 H211 C H sing 1.09 N N
59 C21 H212 C H sing 1.09 N N
60 C24 H241 C H sing 1.09 N N
61 C24 H242 C H sing 1.09 N N
62 C22 H221 C H sing 1.09 N N
63 C22 H222 C H sing 1.09 N N
64 C23 H231 C H sing 1.09 N N
65 C23 H232 C H sing 1.09 N N
66 C26 H261 C H sing 1.09 N N
67 C26 H262 C H sing 1.09 N N
68 C26 H263 C H sing 1.09 N N



KLN : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
KLN 2jjp Open in New Window Bound ligand 1 1
KLN 2v0m Open in New Window Bound ligand 8 1