Chemical Components in the PDB

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MFD : Summary

Code

MFD

One-letter code

X

Molecule name

(2S,3S,8S,9S)-3-AMINO-9-METHOXY-2,6,8-TRIMETHYL-10-PHENYLDECA-4,6-DIENOIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 (2S,3S,4E,6E,8R,9R)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid
OpenEye OEToolkits 1.5.0 (2S,3S,4E,6E,8R,9R)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyl-deca-4,6-dienoic acid

Formula

C20 H29 N O3

Formal charge

0

Molecular weight

331.449 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(C)C(N)/C=C/C(=C/C(C(OC)Cc1ccccc1)C)C
SMILES CACTVS 3.341 CO[CH](Cc1ccccc1)[CH](C)C=C(C)C=C[CH](N)[CH](C)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 CC(C=C(C)C=CC(C(C)C(=O)O)N)C(Cc1ccccc1)OC
Canonical SMILES CACTVS 3.341 CO[C@H](Cc1ccccc1)[C@H](C)\C=C(C)\C=C\[C@H](N)[C@H](C)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C[C@H](\C=C(/C)\C=C\[C@@H]([C@H](C)C(=O)O)N)[C@@H](Cc1ccccc1)OC

IUPAC InChI

InChI=1S/C20H29NO3/c1-14(10-11-18(21)16(3)20(22)23)12-15(2)19(24-4)13-17-8-6-5-7-9-17/h5-12,15-16,18-19H,13,21H2,1-4H3,(H,22,23)/b11-10+,14-12+/t15-,16+,18+,19-/m1/s1

IUPAC InChI key

HJVCHYDYCYBBQX-AWKNMOFVSA-N
MFD

wwPDB Information

Atom count

53 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-08-05

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



MFD : Atoms of Molecule

Total Number of Atoms: 53
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N3 N N N 0 2.208 0.168 -4.617
2 C1 C C2 S N N 0 -0.059 0.42 -5.505
3 C C C1 N N N 0 0.362 -0.224 -6.801
4 O O O1 N N N 0 1.254 -1.039 -6.807
5 OXT O OXT N N Y 0 -0.251 0.108 -7.947
6 CA C C3 S N N 0 0.793 -0.129 -4.36
7 CM2 C CM2 N N N 0 -1.533 0.11 -5.238
8 C7 C C7 N N N 0 -0.948 -0.356 0.195
9 C6 C C6 N N N 0 -0.494 0.393 -0.802
10 C5 C C5 N N N 0 -0.082 -0.235 -2.067
11 C4 C C4 N N N 0 0.371 0.514 -3.065
12 C' C C' N N N 0 -0.994 0.787 3.845
13 C9 C C9 R N N 0 -0.548 -0.009 2.618
14 C8 C C8 R N N 0 -1.482 0.295 1.445
15 C4' C C4' N Y N 0 1.612 -0.063 7.12
16 C3' C C3' N Y N 0 1.9 0.98 6.26
17 C2' C C2' N Y N 0 1.057 1.255 5.2
18 C1' C C1' N Y N 0 -0.074 0.487 5.0
19 C6' C C6' N Y N 0 -0.365 -0.552 5.864
20 C5' C C5' N Y N 0 0.48 -0.83 6.921
21 O9 O O9 N N N 0 -0.595 -1.406 2.914
22 CM9 C CM9 N N N 0 0.735 -1.905 2.769
23 CM8 C CM8 N N N 0 -2.878 -0.252 1.749
24 CM6 C CM6 N N N 0 -0.401 1.889 -0.64
25 H H HN31 N N N 0 2.719 -0.117 -3.795
26 H2 H HN32 N N Y 0 2.288 1.172 -4.673
27 H1 H H2 N N N 0 0.078 1.499 -5.575
28 HXT H HXT N N Y 0 0.019 -0.305 -8.778
29 HA H H3 N N N 0 0.656 -1.208 -4.291
30 HM21 H HM21 N N N 0 -1.67 -0.968 -5.169
31 HM22 H HM22 N N N 0 -1.838 0.576 -4.301
32 HM23 H HM23 N N N 0 -2.141 0.502 -6.054
33 H7 H H7 N N N 0 -0.934 -1.432 0.111
34 H5 H H5 N N N 0 -0.148 -1.306 -2.184
35 H4 H H4 N N N 0 0.437 1.586 -2.949
36 H'1 H H'1 N N N 0 -0.958 1.853 3.619
37 H'2 H H'2 N N N 0 -2.014 0.506 4.11
38 H9 H H9 N N N 0 0.471 0.271 2.353
39 H8 H H8 N N N 0 -1.539 1.373 1.296
40 H4' H H4' N N N 0 2.272 -0.278 7.948
41 H3' H H3' N N N 0 2.785 1.579 6.416
42 H2' H H2' N N N 0 1.282 2.07 4.528
43 H6' H H6' N N N 0 -1.25 -1.152 5.708
44 H5' H H5' N N N 0 0.255 -1.645 7.593
45 HM91 H HM91 N N N 0 0.764 -2.954 3.063
46 HM92 H HM92 N N N 0 1.047 -1.81 1.728
47 HM93 H HM93 N N N 0 1.409 -1.33 3.404
48 HM81 H HM81 N N N 0 -2.821 -1.33 1.897
49 HM82 H HM82 N N N 0 -3.264 0.218 2.652
50 HM83 H HM83 N N N 0 -3.543 -0.035 0.913
51 HM61 H HM61 N N N 0 -0.667 2.16 0.381
52 HM62 H HM62 N N N 0 0.617 2.215 -0.849
53 HM63 H HM63 N N N 0 -1.088 2.373 -1.334



MFD : Chemical Bonds

Total Number of Bonds: 53
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N CA N C sing 1.47 N N
2 N H N H sing 1.01 N N
3 N H2 N H sing 1.01 N N
4 C1 C C C sing 1.51 N N
5 C1 CA C C sing 1.53 N N
6 C1 CM2 C C sing 1.53 N N
7 C1 H1 C H sing 1.09 N N
8 C O C O doub 1.21 N N
9 C OXT C O sing 1.34 N N
10 OXT HXT O H sing 0.97 N N
11 CA C4 C C sing 1.51 N N
12 CA HA C H sing 1.09 N N
13 CM2 HM21 C H sing 1.09 N N
14 CM2 HM22 C H sing 1.09 N N
15 CM2 HM23 C H sing 1.09 N N
16 C7 C6 C C doub 1.33 E N
17 C7 C8 C C sing 1.51 N N
18 C7 H7 C H sing 1.08 N N
19 C6 C5 C C sing 1.47 N N
20 C6 CM6 C C sing 1.51 N N
21 C5 C4 C C doub 1.33 E N
22 C5 H5 C H sing 1.08 N N
23 C4 H4 C H sing 1.08 N N
24 C' C9 C C sing 1.53 N N
25 C' C1' C C sing 1.51 N N
26 C' H'1 C H sing 1.09 N N
27 C' H'2 C H sing 1.09 N N
28 C9 C8 C C sing 1.53 N N
29 C9 O9 C O sing 1.43 N N
30 C9 H9 C H sing 1.09 N N
31 C8 CM8 C C sing 1.53 N N
32 C8 H8 C H sing 1.09 N N
33 C4' C3' C C doub 1.38 N Y
34 C4' C5' C C sing 1.38 N Y
35 C4' H4' C H sing 1.08 N N
36 C3' C2' C C sing 1.38 N Y
37 C3' H3' C H sing 1.08 N N
38 C2' C1' C C doub 1.38 N Y
39 C2' H2' C H sing 1.08 N N
40 C1' C6' C C sing 1.38 N Y
41 C6' C5' C C doub 1.38 N Y
42 C6' H6' C H sing 1.08 N N
43 C5' H5' C H sing 1.08 N N
44 O9 CM9 O C sing 1.43 N N
45 CM9 HM91 C H sing 1.09 N N
46 CM9 HM92 C H sing 1.09 N N
47 CM9 HM93 C H sing 1.09 N N
48 CM8 HM81 C H sing 1.09 N N
49 CM8 HM82 C H sing 1.09 N N
50 CM8 HM83 C H sing 1.09 N N
51 CM6 HM61 C H sing 1.09 N N
52 CM6 HM62 C H sing 1.09 N N
53 CM6 HM63 C H sing 1.09 N N



MFD : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
MFD 1ay3 Open in New Window Polymer component 1 1