Chemical Components in the PDB

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X0B : Summary

Code

X0B

One-letter code

X

Molecule name

5-[3-[4-(aminomethyl)phenoxy]propyl]-2-[(8E)-8-(1,3-benzothiazol-2-ylhydrazinylidene)-6,7-dihydro-5H-naphthalen-2-yl]-1,3-thiazole-4-carboxylic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 5-{3-[4-(aminomethyl)phenoxy]propyl}-2-{(8E)-8-[2-(1,3-benzothiazol-2-yl)hydrazinylidene]-5,6,7,8-tetrahydronaphthalen-2-yl}-1,3-thiazole-4-carboxylic acid
OpenEye OEToolkits 1.9.2 5-[3-[4-(aminomethyl)phenoxy]propyl]-2-[(8E)-8-(1,3-benzothiazol-2-ylhydrazinylidene)-6,7-dihydro-5H-naphthalen-2-yl]-1,3-thiazole-4-carboxylic acid

Formula

C31 H29 N5 O3 S2

Formal charge

0

Molecular weight

583.724 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)c1nc(sc1CCCOc2ccc(cc2)CN)c3ccc6c(c3)/C(=N/Nc4nc5ccccc5s4)CCC6
SMILES CACTVS 3.385 NCc1ccc(OCCCc2sc(nc2C(O)=O)c3ccc4CCCC(=NNc5sc6ccccc6n5)c4c3)cc1
SMILES OpenEye OEToolkits 1.9.2 c1ccc2c(c1)nc(s2)NN=C3CCCc4c3cc(cc4)c5nc(c(s5)CCCOc6ccc(cc6)CN)C(=O)O
Canonical SMILES CACTVS 3.385 NCc1ccc(OCCCc2sc(nc2C(O)=O)c3ccc4CCC\C(=N/Nc5sc6ccccc6n5)c4c3)cc1
Canonical SMILES OpenEye OEToolkits 1.9.2 c1ccc2c(c1)nc(s2)N/N=C/3\CCCc4c3cc(cc4)c5nc(c(s5)CCCOc6ccc(cc6)CN)C(=O)O

IUPAC InChI

InChI=1S/C31H29N5O3S2/c32-18-19-10-14-22(15-11-19)39-16-4-9-27-28(30(37)38)34-29(40-27)21-13-12-20-5-3-7-24(23(20)17-21)35-36-31-33-25-6-1-2-8-26(25)41-31/h1-2,6,8,10-15,17H,3-5,7,9,16,18,32H2,(H,33,36)(H,37,38)/b35-24+

IUPAC InChI key

JKMWZKPAXZBYEH-JWHWKPFMSA-N
X0B

wwPDB Information

Atom count

70 (41 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-02-04

Last modified at

2014-09-05

Status

Released

Obsoleted

Not Assigned



X0B : 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 C C C N Y N 0 5.266 5.542 -0.147
2 C1 C C1 N Y N 0 6.627 5.801 -0.232
3 C10 C C10 N N N 0 4.713 -5.115 -0.714
4 C11 C C11 N Y N 0 3.51 -4.274 -0.379
5 C12 C C12 N Y N 0 3.623 -2.905 -0.131
6 C13 C C13 N Y N 0 2.492 -2.151 0.18
7 C14 C C14 N Y N 0 1.247 -2.771 0.25
8 C15 C C15 N Y N 0 1.143 -4.14 -0.0030
9 C16 C C16 N Y N 0 2.266 -4.878 -0.314
10 C17 C C17 N Y N 0 0.041 -1.982 0.585
11 C18 C C18 N Y N 0 -1.161 -0.189 1.117
12 C19 C C19 N N N 0 -1.348 1.238 1.424
13 C2 C C2 N Y N 0 7.523 4.757 -0.3
14 C20 C C20 N Y N 0 -2.195 -1.077 1.102
15 C21 C C21 N N N 0 -3.637 -0.746 1.389
16 C22 C C22 N N N 0 -4.341 -0.361 0.086
17 C23 C C23 N N N 0 -5.805 -0.026 0.377
18 C25 C C25 N Y N 0 -7.778 0.663 -0.757
19 C26 C C26 N Y N 0 -8.425 0.635 0.47
20 C27 C C27 N Y N 0 -9.761 0.975 0.553
21 C28 C C28 N Y N 0 -10.456 1.334 -0.587
22 C29 C C29 N Y N 0 -9.815 1.357 -1.812
23 C3 C C3 N Y N 0 7.068 3.441 -0.285
24 C30 C C30 N Y N 0 -8.478 1.023 -1.899
25 C31 C C31 N N N 0 -11.915 1.699 -0.495
26 C4 C C4 N Y N 0 5.7 3.166 -0.2
27 C5 C C5 N Y N 0 4.801 4.251 -0.132
28 C6 C C6 N Y N 0 6.424 1.027 -0.269
29 C7 C C7 N N N 0 4.944 -2.243 -0.209
30 C8 C C8 N N N 0 6.169 -3.129 -0.298
31 C9 C C9 N N N 0 5.845 -4.262 -1.28
32 H H H N N N 0 4.567 6.363 -0.094
33 H1 H H1 N N N 0 -0.459 2.999 1.637
34 H101 H H101 N N N 0 5.06 -5.615 0.19
35 H102 H H102 N N N 0 4.429 -5.866 -1.45
36 H13 H H13 N N N 0 2.582 -1.092 0.371
37 H15 H H15 N N N 0 0.178 -4.624 0.044
38 H16 H H16 N N N 0 2.174 -5.937 -0.507
39 H2 H H2 N N N 0 8.582 4.961 -0.366
40 H211 H H211 N N N 0 -4.129 -1.616 1.824
41 H212 H H212 N N N 0 -3.687 0.088 2.089
42 H221 H H221 N N N 0 -3.848 0.508 -0.35
43 H222 H H222 N N N 0 -4.291 -1.195 -0.614
44 H231 H H231 N N N 0 -6.297 -0.895 0.812
45 H232 H H232 N N N 0 -5.854 0.808 1.077
46 H26 H H26 N N N 0 -7.883 0.351 1.36
47 H27 H H27 N N N 0 -10.264 0.958 1.509
48 H29 H H29 N N N 0 -10.361 1.637 -2.701
49 H30 H H30 N N N 0 -7.977 1.041 -2.856
50 H311 H H311 N N N 0 -12.119 2.137 0.483
51 H312 H H312 N N N 0 -12.16 2.42 -1.274
52 H41N H H41N N N N 0 -13.718 0.711 -0.612
53 H42N H H42N N N N 0 -12.517 0.031 -1.541
54 H5 H H5 N N N 0 3.739 4.065 -0.067
55 H81C H H81C N N N 0 6.399 -3.543 0.684
56 H82C H H82C N N N 0 7.018 -2.552 -0.665
57 H91C H H91C N N N 0 6.729 -4.883 -1.424
58 H92C H H92C N N N 0 5.538 -3.838 -2.236
59 HA H HA N N N 0 7.108 -0.9 -0.334
60 HB H HB N N N 0 6.983 6.82 -0.243
61 N N N N Y N 0 5.43 1.846 -0.202
62 N1 N N1 N N N 0 6.312 -0.349 -0.277
63 N2 N N2 N N N 0 5.049 -0.95 -0.202
64 N3 N N3 N Y N 0 0.026 -0.71 0.837
65 N4 N N4 N N N 0 -12.734 0.492 -0.67
66 O O O N N N 0 -2.458 1.666 1.674
67 O1 O O1 N N N 0 -0.287 2.071 1.429
68 O24 O O24 N N N 0 -6.462 0.334 -0.84
69 S S S N Y N 0 7.94 1.912 -0.357
70 S1 S S1 N Y N 0 -1.591 -2.627 0.706



X0B : Chemical Bonds

Total Number of Bonds: 75
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1 C19 O C sing 1.35 N N
2 C19 O C O doub 1.22 N N
3 C19 C18 C C sing 1.47 N N
4 C18 N3 C N sing 1.33 N Y
5 C18 C20 C C doub 1.36 N Y
6 N3 C17 N C doub 1.3 N Y
7 C20 C21 C C sing 1.51 N N
8 C20 S1 C S sing 1.71 N Y
9 C21 C22 C C sing 1.53 N N
10 C22 C23 C C sing 1.53 N N
11 C23 O24 C O sing 1.43 N N
12 O24 C25 O C sing 1.36 N N
13 C25 C30 C C sing 1.39 N Y
14 C25 C26 C C doub 1.39 N Y
15 C30 C29 C C doub 1.38 N Y
16 C29 C28 C C sing 1.38 N Y
17 C28 C31 C C sing 1.51 N N
18 C28 C27 C C doub 1.38 N Y
19 C31 N4 C N sing 1.47 N N
20 C27 C26 C C sing 1.38 N Y
21 S1 C17 S C sing 1.76 N Y
22 C17 C14 C C sing 1.48 N N
23 C14 C15 C C sing 1.4 N Y
24 C14 C13 C C doub 1.39 N Y
25 C15 C16 C C doub 1.38 N Y
26 C16 C11 C C sing 1.38 N Y
27 C11 C10 C C sing 1.51 N N
28 C11 C12 C C doub 1.4 N Y
29 C10 C9 C C sing 1.53 N N
30 C9 C8 C C sing 1.53 N N
31 C8 C7 C C sing 1.51 N N
32 C13 C12 C C sing 1.39 N Y
33 C12 C7 C C sing 1.48 N N
34 C7 N2 C N doub 1.3 E N
35 N2 N1 N N sing 1.4 N N
36 N1 C6 N C sing 1.38 N N
37 C6 S C S sing 1.76 N Y
38 C6 N C N doub 1.29 N Y
39 S C3 S C sing 1.76 N Y
40 C3 C2 C C sing 1.39 N Y
41 C3 C4 C C doub 1.4 N Y
42 C2 C1 C C doub 1.38 N Y
43 C1 C C C sing 1.39 N Y
44 N C4 N C sing 1.35 N Y
45 C4 C5 C C sing 1.41 N Y
46 C5 C C C doub 1.37 N Y
47 O1 H1 O H sing 0.97 N N
48 C21 H211 C H sing 1.09 N N
49 C21 H212 C H sing 1.09 N N
50 C22 H221 C H sing 1.09 N N
51 C22 H222 C H sing 1.09 N N
52 C23 H231 C H sing 1.09 N N
53 C23 H232 C H sing 1.09 N N
54 C30 H30 C H sing 1.08 N N
55 C26 H26 C H sing 1.08 N N
56 C29 H29 C H sing 1.08 N N
57 C31 H311 C H sing 1.09 N N
58 C31 H312 C H sing 1.09 N N
59 C27 H27 C H sing 1.08 N N
60 N4 H41N N H sing 1.01 N N
61 N4 H42N N H sing 1.01 N N
62 C15 H15 C H sing 1.08 N N
63 C13 H13 C H sing 1.08 N N
64 C16 H16 C H sing 1.08 N N
65 C10 H101 C H sing 1.09 N N
66 C10 H102 C H sing 1.09 N N
67 C9 H91C C H sing 1.09 N N
68 C9 H92C C H sing 1.09 N N
69 C8 H81C C H sing 1.09 N N
70 C8 H82C C H sing 1.09 N N
71 N1 HA N H sing 0.97 N N
72 C2 H2 C H sing 1.08 N N
73 C1 HB C H sing 1.08 N N
74 C H C H sing 1.08 N N
75 C5 H5 C H sing 1.08 N N



X0B : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
X0B 3zlr Open in New Window Bound ligand 2 1