Chemical Components in the PDB

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QRH : Summary

Code

QRH

One-letter code

X

Molecule name

(2~{E},4~{E})-5-(1,3-benzodioxol-5-yl)-~{N}-[6-(triphenyl-$l^{5}-phosphanyl)hexyl]penta-2,4-dienamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (2~{E},4~{E})-5-(1,3-benzodioxol-5-yl)-~{N}-[6-(triphenyl-$l^{5}-phosphanyl)hexyl]penta-2,4-dienamide

Formula

C36 H38 N O3 P

Formal charge

0

Molecular weight

563.666 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 O=C(NCCCCCC[PH](c1ccccc1)(c2ccccc2)c3ccccc3)C=CC=Cc4ccc5OCOc5c4
SMILES OpenEye OEToolkits 2.0.7 c1ccc(cc1)P(CCCCCCNC(=O)C=CC=Cc2ccc3c(c2)OCO3)(c4ccccc4)c5ccccc5
Canonical SMILES CACTVS 3.385 O=C(NCCCCCC[PH](c1ccccc1)(c2ccccc2)c3ccccc3)/C=C/C=C/c4ccc5OCOc5c4
Canonical SMILES OpenEye OEToolkits 2.0.7 c1ccc(cc1)P(CCCCCCNC(=O)/C=C/C=C/c2ccc3c(c2)OCO3)(c4ccccc4)c5ccccc5

IUPAC InChI

InChI=1S/C36H38NO3P/c38-36(23-13-12-16-30-24-25-34-35(28-30)40-29-39-34)37-26-14-1-2-15-27-41(31-17-6-3-7-18-31,32-19-8-4-9-20-32)33-21-10-5-11-22-33/h3-13,16-25,28,41H,1-2,14-15,26-27,29H2,(H,37,38)/b16-12+,23-13+

IUPAC InChI key

XYBUESNIYRZZQB-XSDFDVSCSA-N
QRH

wwPDB Information

Atom count

79 (41 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-07-29

Last modified at

2021-06-04

Status

Released

Obsoleted

Not Assigned



QRH : Atoms of Molecule

Total Number of Atoms: 79
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C02 C C1 N N N 0 -3.967 -0.667 -0.276
2 C03 C C2 N N N 0 -5.222 -0.013 -0.231
3 O01 O O1 N N N 0 -3.915 -1.884 -0.274
4 C04 C C3 N N N 0 -6.366 -0.742 -0.186
5 C05 C C4 N N N 0 -7.617 -0.09 -0.142
6 C06 C C5 N N N 0 -8.758 -0.817 -0.098
7 C07 C C6 N Y N 0 -10.06 -0.139 -0.051
8 C08 C C7 N Y N 0 -11.242 -0.888 -0.005
9 C09 C C8 N Y N 0 -12.462 -0.245 0.038
10 C11 C C9 N N N 0 -14.552 0.372 0.528
11 C13 C C10 N Y N 0 -12.518 1.15 0.037
12 C14 C C11 N Y N 0 -11.346 1.893 -0.008
13 C15 C C12 N Y N 0 -10.123 1.26 -0.047
14 C17 C C13 N N N 0 -1.533 -0.62 -0.378
15 C18 C C14 N N N 0 -0.415 0.423 -0.428
16 C19 C C15 N N N 0 0.94 -0.284 -0.482
17 C20 C C16 N N N 0 2.058 0.76 -0.532
18 C21 C C17 N N N 0 3.414 0.053 -0.587
19 C22 C C18 N N N 0 4.531 1.096 -0.637
20 C24 C C19 N Y N 0 7.744 1.217 -1.032
21 C25 C C20 N Y N 0 8.931 0.563 -1.303
22 C26 C C21 N Y N 0 10.081 1.291 -1.546
23 C27 C C22 N Y N 0 10.044 2.672 -1.516
24 C31 C C26 N Y N 0 7.501 -2.205 -0.127
25 C28 C C23 N Y N 0 8.856 3.326 -1.245
26 C29 C C24 N Y N 0 7.705 2.598 -1.009
27 C30 C C25 N Y N 0 6.29 -1.617 -0.442
28 C32 C C27 N Y N 0 7.575 -3.571 0.072
29 C33 C C28 N Y N 0 6.438 -4.349 -0.043
30 C34 C C29 N Y N 0 5.227 -3.76 -0.357
31 C35 C C30 N Y N 0 5.153 -2.395 -0.557
32 C36 C C31 N Y N 0 6.404 0.504 1.134
33 C37 C C32 N Y N 0 5.297 0.551 1.961
34 C38 C C33 N Y N 0 5.457 0.752 3.319
35 C39 C C34 N Y N 0 6.723 0.906 3.851
36 C40 C C35 N Y N 0 7.831 0.859 3.024
37 C41 C C36 N Y N 0 7.671 0.653 1.667
38 N16 N N1 N N N 0 -2.831 0.057 -0.325
39 O10 O O2 N N N 0 -13.738 -0.731 0.087
40 O12 O O3 N N N 0 -13.826 1.533 0.084
41 P23 P P1 N N N 0 6.188 0.232 -0.703
42 H1 H H1 N N N 0 -5.269 1.066 -0.232
43 H2 H H2 N N N 0 -6.32 -1.821 -0.185
44 H3 H H3 N N N 0 -7.663 0.989 -0.143
45 H4 H H4 N N N 0 -8.711 -1.896 -0.097
46 H5 H H5 N N N 0 -11.198 -1.967 -0.005
47 H6 H H6 N N N 0 -15.535 0.333 0.059
48 H7 H H7 N N N 0 -14.646 0.368 1.614
49 H8 H H8 N N N 0 -11.393 2.972 -0.009
50 H9 H H9 N N N 0 -9.214 1.842 -0.082
51 H10 H H10 N N N 0 -1.486 -1.247 -1.268
52 H11 H H11 N N N 0 -1.411 -1.241 0.51
53 H12 H H12 N N N 0 -0.538 1.044 -1.315
54 H13 H H13 N N N 0 -0.463 1.049 0.463
55 H14 H H14 N N N 0 1.062 -0.905 0.405
56 H15 H H15 N N N 0 0.988 -0.91 -1.373
57 H16 H H16 N N N 0 1.936 1.381 -1.42
58 H17 H H17 N N N 0 2.01 1.386 0.359
59 H18 H H18 N N N 0 3.536 -0.568 0.301
60 H19 H H19 N N N 0 3.461 -0.574 -1.477
61 H20 H H20 N N N 0 4.41 1.717 -1.524
62 H21 H H21 N N N 0 4.484 1.722 0.254
63 H22 H H22 N N N 0 8.961 -0.516 -1.326
64 H26 H H26 N N N 0 6.778 3.109 -0.797
65 H23 H H23 N N N 0 11.009 0.78 -1.757
66 H24 H H24 N N N 0 10.942 3.241 -1.705
67 H25 H H25 N N N 0 8.826 4.405 -1.227
68 H27 H H27 N N N 0 8.389 -1.597 -0.038
69 H28 H H28 N N N 0 8.521 -4.03 0.316
70 H29 H H29 N N N 0 6.496 -5.416 0.112
71 H30 H H30 N N N 0 4.339 -4.368 -0.447
72 H31 H H31 N N N 0 4.207 -1.935 -0.802
73 H32 H H32 N N N 0 4.308 0.43 1.545
74 H33 H H33 N N N 0 4.592 0.789 3.965
75 H34 H H34 N N N 0 6.848 1.064 4.912
76 H35 H H35 N N N 0 8.82 0.98 3.44
77 H36 H H36 N N N 0 8.536 0.612 1.022
78 H37 H H37 N N N 0 -2.873 1.026 -0.326
79 H38 H H38 N N N 0 6.019 0.018 -2.148



QRH : 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 O12 C11 O C sing 1.44 N N
2 O12 C13 O C sing 1.36 N N
3 C11 O10 C O sing 1.44 N N
4 C14 C13 C C doub 1.39 N Y
5 C14 C15 C C sing 1.38 N Y
6 C13 C09 C C sing 1.4 N Y
7 C15 C07 C C doub 1.4 N Y
8 O10 C09 O C sing 1.37 N N
9 C09 C08 C C doub 1.38 N Y
10 C07 C08 C C sing 1.4 N Y
11 C07 C06 C C sing 1.47 N N
12 C06 C05 C C doub 1.35 E N
13 C05 C04 C C sing 1.41 N N
14 C20 C21 C C sing 1.53 N N
15 C20 C19 C C sing 1.53 N N
16 C21 C22 C C sing 1.53 N N
17 C19 C18 C C sing 1.53 N N
18 C28 C29 C C doub 1.38 N Y
19 C28 C27 C C sing 1.38 N Y
20 C04 C03 C C doub 1.36 E N
21 C29 C24 C C sing 1.38 N Y
22 C27 C26 C C doub 1.38 N Y
23 C18 C17 C C sing 1.53 N N
24 C22 P23 C P sing 1.87 N N
25 C03 C02 C C sing 1.42 N N
26 C38 C37 C C doub 1.38 N Y
27 C38 C39 C C sing 1.38 N Y
28 C37 C36 C C sing 1.38 N Y
29 C24 P23 C P sing 1.87 N N
30 C24 C25 C C doub 1.38 N Y
31 C39 C40 C C doub 1.38 N Y
32 C36 P23 C P sing 1.87 N N
33 C36 C41 C C doub 1.38 N Y
34 C26 C25 C C sing 1.38 N Y
35 C02 O01 C O doub 1.22 N N
36 C02 N16 C N sing 1.35 N N
37 P23 C30 P C sing 1.87 N N
38 C40 C41 C C sing 1.38 N Y
39 C17 N16 C N sing 1.46 N N
40 C30 C31 C C doub 1.38 N Y
41 C30 C35 C C sing 1.38 N Y
42 C31 C32 C C sing 1.38 N Y
43 C35 C34 C C doub 1.38 N Y
44 C32 C33 C C doub 1.38 N Y
45 C34 C33 C C sing 1.38 N Y
46 C03 H1 C H sing 1.08 N N
47 C04 H2 C H sing 1.08 N N
48 C05 H3 C H sing 1.08 N N
49 C06 H4 C H sing 1.08 N N
50 C08 H5 C H sing 1.08 N N
51 C11 H6 C H sing 1.09 N N
52 C11 H7 C H sing 1.09 N N
53 C14 H8 C H sing 1.08 N N
54 C15 H9 C H sing 1.08 N N
55 C17 H10 C H sing 1.09 N N
56 C17 H11 C H sing 1.09 N N
57 C18 H12 C H sing 1.09 N N
58 C18 H13 C H sing 1.09 N N
59 C19 H14 C H sing 1.09 N N
60 C19 H15 C H sing 1.09 N N
61 C20 H16 C H sing 1.09 N N
62 C20 H17 C H sing 1.09 N N
63 C21 H18 C H sing 1.09 N N
64 C21 H19 C H sing 1.09 N N
65 C22 H20 C H sing 1.09 N N
66 C22 H21 C H sing 1.09 N N
67 C25 H22 C H sing 1.08 N N
68 C26 H23 C H sing 1.08 N N
69 C27 H24 C H sing 1.08 N N
70 C28 H25 C H sing 1.08 N N
71 C29 H26 C H sing 1.08 N N
72 C31 H27 C H sing 1.08 N N
73 C32 H28 C H sing 1.08 N N
74 C33 H29 C H sing 1.08 N N
75 C34 H30 C H sing 1.08 N N
76 C35 H31 C H sing 1.08 N N
77 C37 H32 C H sing 1.08 N N
78 C38 H33 C H sing 1.08 N N
79 C39 H34 C H sing 1.08 N N
80 C40 H35 C H sing 1.08 N N
81 C41 H36 C H sing 1.08 N N
82 N16 H37 N H sing 0.97 N N
83 P23 H38 P H sing 1.47 N N



QRH : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
QRH 6zwe Open in New Window Bound ligand 1 1
QRH 6zwi Open in New Window Bound ligand 1 1