Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

40P : Summary

Code

40P

One-letter code

X

Molecule name

Pinnatoxin A

Systematic names

ProgramVersionName
ACDLabs 12.01 (1R,3R,7R,10R,11R,14S,23R,24S,26R,31S,32S,33R,34R,35R)-11,34-dihydroxy-11,23,24,35-tetramethyl-16-methylidene-37,38,39,40,41-pentaoxa-21-azaoctacyclo[30.4.1.1~1,33~.1~3,7~.1~7,10~.1~10,14~.0~20,26~.0~26,31~]hentetraconta-20,29-diene-29-carboxylic acid (non-preferred name)

Formula

C41 H61 N O9

Formal charge

0

Molecular weight

711.924 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C8=CC3C1(C(=NCC(C)C(C)C1)CCC/C(=C)CC7OC6(OC2(OC(CCC2)CC45OC3C(O4)C(O)C(C)C5)CC6)C(O)(CC7)C)CC8
SMILES CACTVS 3.385 C[CH]1CN=C2CCCC(=C)C[CH]3CC[C](C)(O)[C]4(CC[C]5(CCC[CH](C[C]67C[CH](C)[CH](O)[CH](O6)[CH](O7)[CH]8C=C(CC[C]28C[CH]1C)C(O)=O)O5)O4)O3
SMILES OpenEye OEToolkits 1.9.2 CC1CC23CCC(=CC2C4C5C(C(CC(O4)(O5)CC6CCCC7(O6)CCC8(O7)C(CCC(O8)CC(=C)CCCC3=NCC1C)(C)O)C)O)C(=O)O
Canonical SMILES CACTVS 3.385 C[C@H]1CN=C2CCCC(=C)C[C@@H]3CC[C@@](C)(O)[C@]4(CC[C@@]5(CCC[C@H](C[C@@]67C[C@@H](C)[C@@H](O)[C@@H](O6)[C@@H](O7)[C@H]8C=C(CC[C@]28C[C@@H]1C)C(O)=O)O5)O4)O3
Canonical SMILES OpenEye OEToolkits 1.9.2 C[C@H]1C[C@]23CCC(=C[C@@H]2[C@H]4[C@H]5[C@@H]([C@@H](C[C@@](O4)(O5)C[C@H]6CCC[C@]7(O6)CC[C@@]8(O7)[C@](CC[C@H](O8)CC(=C)CCCC3=NC[C@@H]1C)(C)O)C)O)C(=O)O

IUPAC InChI

InChI=1S/C41H61NO9/c1-24-8-6-10-32-38(20-25(2)27(4)23-42-32)15-11-28(36(44)45)19-31(38)34-35-33(43)26(3)21-40(49-34,50-35)22-30-9-7-13-39(47-30)16-17-41(51-39)37(5,46)14-12-29(18-24)48-41/h19,25-27,29-31,33-35,43,46H,1,6-18,20-23H2,2-5H3,(H,44,45)/t25-,26+,27-,29-,30+,31+,33+,34-,35+,37+,38+,39+,40+,41+/m0/s1

IUPAC InChI key

ZYFHPTPXLHNGQK-OICTYLSBSA-N
40P

wwPDB Information

Atom count

112 (51 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-01-06

Last modified at

2015-05-29

Status

Released

Obsoleted

Not Assigned



40P : Atoms of Molecule

Total Number of Atoms: 112
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C13 C C1 N N N 0 1.744 -3.087 51.247
2 C18 C C2 N N N 0 -3.067 0.337 52.43
3 C15 C C3 S N N 0 -0.331 -1.868 51.848
4 C17 C C4 R N N 0 -1.8 -0.087 51.708
5 O1 O O1 N N N 0 4.501 -3.229 51.685
6 O3 O O2 N N N 0 4.442 -5.374 51.374
7 C2 C C5 N N N 0 3.872 -4.274 51.419
8 C8 C C6 N N N 0 2.427 -4.242 51.13
9 C9 C C7 N N N 0 1.798 -5.536 50.695
10 C10 C C8 N N N 0 0.342 -5.371 50.253
11 C27 C C9 R N N 0 -0.434 -4.348 51.069
12 C28 C C10 N N N 0 -0.449 -4.825 52.544
13 C46 C C11 S N N 0 -1.773 -4.59 53.298
14 C22 C C12 N N N 0 -1.544 -4.45 54.812
15 C29 C C13 R N N 0 -2.76 -5.713 53.058
16 C6 C C14 N N N 0 -4.198 -5.228 53.253
17 C30 C C15 N N N 0 -2.588 -6.375 51.697
18 N31 N N1 N N N 0 -2.646 -5.318 50.665
19 C32 C C16 N N N 0 -1.812 -4.407 50.378
20 C33 C C17 N N N 0 -2.161 -3.464 49.234
21 C34 C C18 N N N 0 -3.642 -3.412 48.869
22 C35 C C19 N N N 0 -4.45 -2.774 49.983
23 C36 C C20 N N N 0 -5.876 -2.413 49.602
24 C38 C C21 N N N 0 -6.455 -2.897 48.511
25 C37 C C22 N N N 0 -6.65 -1.488 50.517
26 C48 C C23 S N N 0 -6.73 -1.966 51.983
27 C49 C C24 N N N 0 -7.389 -3.326 52.154
28 C50 C C25 N N N 0 -7.634 -3.655 53.631
29 C51 C C26 R N N 0 -8.236 -2.466 54.384
30 O52 O O3 N N N 0 -8.276 -2.764 55.78
31 C53 C C27 N N N 0 -9.649 -2.163 53.86
32 O47 O O4 N N N 0 -7.34 -0.956 52.776
33 C43 C C28 R N N 0 -7.356 -1.267 54.179
34 O44 O O5 N N N 0 -6.002 -1.489 54.638
35 C42 C C29 N N N 0 -7.877 -0.009 54.884
36 C55 C C30 N N N 0 -6.627 0.721 55.301
37 C23 C C31 R N N 0 -5.457 -0.218 55.049
38 O48 O O6 N N N 0 -4.624 0.289 54.01
39 C80 C C32 N N N 0 -4.759 -0.387 56.366
40 C60 C C33 N N N 0 -3.52 -1.241 56.026
41 C81 C C34 N N N 0 -2.688 -0.675 54.848
42 C21 C C35 R N N 0 -3.528 -0.546 53.596
43 O16 O O7 N N N 0 -1.682 -1.503 51.507
44 O65 O O8 N N N 0 -0.662 0.29 52.452
45 C61 C C36 R N N 0 0.379 -0.517 51.914
46 C62 C C37 R N N 0 0.781 0.103 50.567
47 O66 O O9 N N N 0 1.354 1.39 50.808
48 C63 C C38 R N N 0 -0.426 0.263 49.627
49 C67 C C39 N N N 0 -0.173 1.26 48.492
50 C64 C C40 N N N 0 -1.676 0.665 50.382
51 C12 C C41 S N N 0 0.258 -2.96 50.934
52 H1 H H1 N N N 0 2.276 -2.207 51.579
53 H2 H H2 N N N 0 -2.901 1.35 52.825
54 H3 H H3 N N N 0 -3.88 0.361 51.689
55 H4 H H4 N N N 0 -0.337 -2.277 52.869
56 H5 H H5 N N N 0 5.416 -3.438 51.83
57 H6 H H6 N N N 0 1.831 -6.243 51.537
58 H7 H H7 N N N 0 2.377 -5.942 49.852
59 H8 H H8 N N N 0 0.333 -5.054 49.2
60 H9 H H9 N N N 0 -0.162 -6.344 50.347
61 H10 H H10 N N N 0 -0.239 -5.905 52.554
62 H11 H H11 N N N 0 0.348 -4.291 53.082
63 H12 H H12 N N N 0 -2.215 -3.653 52.93
64 H13 H H13 N N N 0 -2.508 -4.284 55.315
65 H14 H H14 N N N 0 -1.082 -5.37 55.199
66 H15 H H15 N N N 0 -0.878 -3.596 55.005
67 H16 H H16 N N N 0 -2.572 -6.483 53.821
68 H17 H H17 N N N 0 -4.295 -4.755 54.241
69 H18 H H18 N N N 0 -4.447 -4.496 52.47
70 H19 H H19 N N N 0 -4.886 -6.084 53.187
71 H20 H H20 N N N 0 -3.395 -7.103 51.531
72 H21 H H21 N N N 0 -1.616 -6.888 51.652
73 H22 H H22 N N N 0 -1.601 -3.786 48.343
74 H23 H H23 N N N 0 -1.844 -2.45 49.519
75 H24 H H24 N N N 0 -3.766 -2.821 47.95
76 H25 H H25 N N N 0 -4.008 -4.436 48.699
77 H26 H H26 N N N 0 -4.488 -3.479 50.827
78 H27 H H27 N N N 0 -3.935 -1.854 50.297
79 H28 H H28 N N N 0 -7.475 -2.631 48.278
80 H29 H H29 N N N 0 -5.906 -3.557 47.856
81 H30 H H30 N N N 0 -6.163 -0.502 50.502
82 H31 H H31 N N N 0 -7.675 -1.397 50.128
83 H32 H H32 N N N 0 -5.691 -2.078 52.327
84 H33 H H33 N N N 0 -8.353 -3.324 51.624
85 H34 H H34 N N N 0 -6.734 -4.096 51.721
86 H35 H H35 N N N 0 -8.328 -4.506 53.696
87 H36 H H36 N N N 0 -6.676 -3.926 54.099
88 H37 H H37 N N N 0 -8.649 -2.028 56.251
89 H38 H H38 N N N 0 -10.069 -1.308 54.409
90 H39 H H39 N N N 0 -9.598 -1.921 52.788
91 H40 H H40 N N N 0 -10.291 -3.044 54.007
92 H41 H H41 N N N 0 -8.477 0.605 54.196
93 H42 H H42 N N N 0 -8.485 -0.276 55.761
94 H43 H H43 N N N 0 -6.51 1.639 54.706
95 H44 H H44 N N N 0 -6.68 0.98 56.369
96 H45 H H45 N N N 0 -4.46 0.588 56.778
97 H46 H H46 N N N 0 -5.406 -0.907 57.087
98 H47 H H47 N N N 0 -3.857 -2.254 55.76
99 H48 H H48 N N N 0 -2.876 -1.291 56.916
100 H49 H H49 N N N 0 -1.845 -1.352 54.646
101 H50 H H50 N N N 0 -2.303 0.317 55.125
102 H51 H H51 N N N 0 -3.862 -1.53 53.236
103 H52 H H52 N N N 0 1.249 -0.572 52.585
104 H53 H H53 N N N 0 1.518 -0.554 50.083
105 H54 H H54 N N N 0 2.101 1.301 51.388
106 H55 H H55 N N N 0 -0.616 -0.718 49.167
107 H56 H H56 N N N 0 0.735 0.969 47.943
108 H57 H H57 N N N 0 -1.033 1.26 47.806
109 H58 H H58 N N N 0 -0.04 2.268 48.912
110 H59 H H59 N N N 0 -1.638 1.745 50.587
111 H60 H H60 N N N 0 -2.556 0.441 49.761
112 H61 H H61 N N N 0 0.151 -2.628 49.891



40P : Chemical Bonds

Total Number of Bonds: 119
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C67 C63 C C sing 1.53 N N
2 C38 C36 C C doub 1.33 N N
3 C34 C33 C C sing 1.53 N N
4 C34 C35 C C sing 1.52 N N
5 C33 C32 C C sing 1.52 N N
6 C36 C35 C C sing 1.52 N N
7 C36 C37 C C sing 1.51 N N
8 C63 C64 C C sing 1.51 N N
9 C63 C62 C C sing 1.54 N N
10 C10 C9 C C sing 1.53 N N
11 C10 C27 C C sing 1.52 N N
12 C32 N31 C N doub 1.27 N N
13 C32 C27 C C sing 1.54 N N
14 C64 C17 C C sing 1.53 N N
15 C37 C48 C C sing 1.54 N N
16 C62 O66 C O sing 1.43 N N
17 C62 C61 C C sing 1.54 N N
18 N31 C30 N C sing 1.48 N N
19 C9 C8 C C sing 1.5 N N
20 C12 C27 C C sing 1.56 N N
21 C12 C13 C C sing 1.52 N N
22 C12 C15 C C sing 1.54 N N
23 C27 C28 C C sing 1.55 N N
24 C8 C13 C C doub 1.35 N N
25 C8 C2 C C sing 1.47 N N
26 O3 C2 O C doub 1.24 N N
27 C2 O1 C O sing 1.25 N N
28 O16 C17 O C sing 1.44 N N
29 O16 C15 O C sing 1.44 N N
30 C30 C29 C C sing 1.52 N N
31 C17 C18 C C sing 1.52 N N
32 C17 O65 C O sing 1.41 N N
33 C15 C61 C C sing 1.53 N N
34 C61 O65 C O sing 1.42 N N
35 C48 C49 C C sing 1.52 N N
36 C48 O47 C O sing 1.42 N N
37 C49 C50 C C sing 1.53 N N
38 C18 C21 C C sing 1.53 N N
39 C28 C46 C C sing 1.54 N N
40 O47 C43 O C sing 1.44 N N
41 C29 C6 C C sing 1.53 N N
42 C29 C46 C C sing 1.51 N N
43 C46 C22 C C sing 1.54 N N
44 C21 O48 C O sing 1.44 N N
45 C21 C81 C C sing 1.51 N N
46 C50 C51 C C sing 1.53 N N
47 C53 C51 C C sing 1.54 N N
48 O48 C23 O C sing 1.42 N N
49 C43 C51 C C sing 1.5 N N
50 C43 O44 C O sing 1.45 N N
51 C43 C42 C C sing 1.53 N N
52 C51 O52 C O sing 1.43 N N
53 O44 C23 O C sing 1.44 N N
54 C81 C60 C C sing 1.55 N N
55 C42 C55 C C sing 1.51 N N
56 C23 C55 C C sing 1.52 N N
57 C23 C80 C C sing 1.5 N N
58 C60 C80 C C sing 1.54 N N
59 C13 H1 C H sing 1.08 N N
60 C18 H2 C H sing 1.1 N N
61 C18 H3 C H sing 1.1 N N
62 C15 H4 C H sing 1.1 N N
63 O1 H5 O H sing 0.95 N N
64 C9 H6 C H sing 1.1 N N
65 C9 H7 C H sing 1.1 N N
66 C10 H8 C H sing 1.1 N N
67 C10 H9 C H sing 1.1 N N
68 C28 H10 C H sing 1.1 N N
69 C28 H11 C H sing 1.1 N N
70 C46 H12 C H sing 1.1 N N
71 C22 H13 C H sing 1.1 N N
72 C22 H14 C H sing 1.1 N N
73 C22 H15 C H sing 1.1 N N
74 C29 H16 C H sing 1.1 N N
75 C6 H17 C H sing 1.1 N N
76 C6 H18 C H sing 1.1 N N
77 C6 H19 C H sing 1.1 N N
78 C30 H20 C H sing 1.1 N N
79 C30 H21 C H sing 1.1 N N
80 C33 H22 C H sing 1.1 N N
81 C33 H23 C H sing 1.1 N N
82 C34 H24 C H sing 1.1 N N
83 C34 H25 C H sing 1.1 N N
84 C35 H26 C H sing 1.1 N N
85 C35 H27 C H sing 1.1 N N
86 C38 H28 C H sing 1.08 N N
87 C38 H29 C H sing 1.08 N N
88 C37 H30 C H sing 1.1 N N
89 C37 H31 C H sing 1.1 N N
90 C48 H32 C H sing 1.1 N N
91 C49 H33 C H sing 1.1 N N
92 C49 H34 C H sing 1.1 N N
93 C50 H35 C H sing 1.1 N N
94 C50 H36 C H sing 1.1 N N
95 O52 H37 O H sing 0.95 N N
96 C53 H38 C H sing 1.1 N N
97 C53 H39 C H sing 1.1 N N
98 C53 H40 C H sing 1.1 N N
99 C42 H41 C H sing 1.1 N N
100 C42 H42 C H sing 1.1 N N
101 C55 H43 C H sing 1.1 N N
102 C55 H44 C H sing 1.1 N N
103 C80 H45 C H sing 1.1 N N
104 C80 H46 C H sing 1.1 N N
105 C60 H47 C H sing 1.1 N N
106 C60 H48 C H sing 1.1 N N
107 C81 H49 C H sing 1.1 N N
108 C81 H50 C H sing 1.1 N N
109 C21 H51 C H sing 1.1 N N
110 C61 H52 C H sing 1.1 N N
111 C62 H53 C H sing 1.1 N N
112 O66 H54 O H sing 0.95 N N
113 C63 H55 C H sing 1.1 N N
114 C67 H56 C H sing 1.1 N N
115 C67 H57 C H sing 1.1 N N
116 C67 H58 C H sing 1.1 N N
117 C64 H59 C H sing 1.1 N N
118 C64 H60 C H sing 1.1 N N
119 C12 H61 C H sing 1.1 N N



40P : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
40P 4xhe Open in New Window Bound ligand 10 1