Chemical Components in the PDB

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MIY : Summary

Code

MIY

One-letter code

X

Molecule name

(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE

Synonyms

MINOCYCLINE

Systematic names

ProgramVersionName
ACDLabs 10.04 (4S,4aS,5aR,12aS)-4,7-bis(dimethylamino)-3,10,12,12a-tetrahydroxy-1,11-dioxo-1,4,4a,5,5a,6,11,12a-octahydrotetracene-2-carboxamide
OpenEye OEToolkits 1.5.0 (4S,4aS,5aR,12aS)-4,7-bis(dimethylamino)-3,10,12,12a-tetrahydroxy-1,11-dioxo-4a,5,5a,6-tetrahydro-4H-tetracene-2-carboxamide

Formula

C23 H27 N3 O7

Formal charge

0

Molecular weight

457.476 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(N)C1=C(O)C(N(C)C)C2CC4C(=C(O)C2(O)C1=O)C(=O)c3c(c(ccc3O)N(C)C)C4
SMILES CACTVS 3.341 CN(C)[CH]1[CH]2C[CH]3Cc4c(ccc(O)c4C(=O)C3=C(O)[C]2(O)C(=O)C(=C1O)C(N)=O)N(C)C
SMILES OpenEye OEToolkits 1.5.0 CN(C)c1ccc(c2c1CC3CC4C(C(=C(C(=O)C4(C(=C3C2=O)O)O)C(=O)N)O)N(C)C)O
Canonical SMILES CACTVS 3.341 CN(C)[C@H]1[C@@H]2C[C@@H]3Cc4c(ccc(O)c4C(=O)C3=C(O)[C@]2(O)C(=O)C(=C1O)C(N)=O)N(C)C
Canonical SMILES OpenEye OEToolkits 1.5.0 CN(C)c1ccc(c2c1C[C@H]3C[C@H]4[C@@H](C(=C(C(=O)[C@]4(C(=C3C2=O)O)O)C(=O)N)O)N(C)C)O

IUPAC InChI

InChI=1S/C23H27N3O7/c1-25(2)12-5-6-13(27)15-10(12)7-9-8-11-17(26(3)4)19(29)16(22(24)32)21(31)23(11,33)20(30)14(9)18(15)28/h5-6,9,11,17,27,29-30,33H,7-8H2,1-4H3,(H2,24,32)/t9-,11-,17-,23-/m0/s1

IUPAC InChI key

DYKFCLLONBREIL-KVUCHLLUSA-N
MIY

wwPDB Information

Atom count

60 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2006-06-09

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



MIY : Atoms of Molecule

Total Number of Atoms: 60
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O8 O O8 N N N 0
2 C21 C C21 N N N 0
3 N2 N N2 N N N 0
4 C2 C C2 N N N 0
5 C1 C C1 N N N 0
6 O1 O O1 N N N 0
7 C3 C C3 N N N 0
8 O2 O O2 N N N 0
9 C4 C C4 S N N 0
10 N1 N N1 N N N 0
11 C20 C C20 N N N 0
12 C19 C C19 N N N 0
13 C5 C C5 S N N 0
14 C18 C C18 S N N 0
15 O7 O O7 N N N 0
16 C17 C C17 N N N 0
17 O6 O O6 N N N 0
18 C16 C C16 N N N 0
19 C7 C C7 R N N 0
20 C6 C C6 N N N 0
21 C15 C C15 N N N 0
22 O5 O O5 N N N 0
23 C14 C C14 N Y N 0
24 C9 C C9 N Y N 0
25 C8 C C8 N N N 0
26 C13 C C13 N Y N 0
27 O4 O O4 N N N 0
28 C12 C C12 N Y N 0
29 C11 C C11 N Y N 0
30 C10 C C10 N Y N 0
31 N7 N N7 N N N 0
32 CN7 C CN7 N N N 0
33 C71 C C71 N N N 0
34 HN21 H 1HN2 N N N 0
35 HN22 H 2HN2 N N N 0
36 HO2 H HO2 N N N 0
37 H4 H H4 N N N 0
38 H201 H 1H20 N N N 0
39 H202 H 2H20 N N N 0
40 H203 H 3H20 N N N 0
41 H191 H 1H19 N N N 0
42 H192 H 2H19 N N N 0
43 H193 H 3H19 N N N 0
44 H5 H H5 N N N 0
45 HO7 H HO7 N N N 0
46 HO6 H HO6 N N N 0
47 H7 H H7 N N N 0
48 H61 H 1H6 N N N 0
49 H62 H 2H6 N N N 0
50 H81 H 1H8 N N N 0
51 H82 H 2H8 N N N 0
52 HO4 H HO4 N N N 0
53 H12 H H12 N N N 0
54 H11 H H11 N N N 0
55 HN71 H 1HN7 N N N 0
56 HN72 H 2HN7 N N N 0
57 HN73 H 3HN7 N N N 0
58 H711 H 1H71 N N N 0
59 H712 H 2H71 N N N 0
60 H713 H 3H71 N N N 0



MIY : Chemical Bonds

Total Number of Bonds: 63
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O8 C21 O C doub N N
2 C21 N2 C N sing N N
3 C21 C2 C C sing N N
4 N2 HN21 N H sing N N
5 N2 HN22 N H sing N N
6 C2 C1 C C sing N N
7 C2 C3 C C doub N N
8 C1 O1 C O doub N N
9 C1 C18 C C sing N N
10 C3 O2 C O sing N N
11 C3 C4 C C sing N N
12 O2 HO2 O H sing N N
13 C4 N1 C N sing N N
14 C4 C5 C C sing N N
15 C4 H4 C H sing N N
16 N1 C20 N C sing N N
17 N1 C19 N C sing N N
18 C20 H201 C H sing N N
19 C20 H202 C H sing N N
20 C20 H203 C H sing N N
21 C19 H191 C H sing N N
22 C19 H192 C H sing N N
23 C19 H193 C H sing N N
24 C5 C18 C C sing N N
25 C5 C6 C C sing N N
26 C5 H5 C H sing N N
27 C18 O7 C O sing N N
28 C18 C17 C C sing N N
29 O7 HO7 O H sing N N
30 C17 O6 C O sing N N
31 C17 C16 C C doub N N
32 O6 HO6 O H sing N N
33 C16 C7 C C sing N N
34 C16 C15 C C sing N N
35 C7 C6 C C sing N N
36 C7 C8 C C sing N N
37 C7 H7 C H sing N N
38 C6 H61 C H sing N N
39 C6 H62 C H sing N N
40 C15 O5 C O doub N N
41 C15 C14 C C sing N N
42 C14 C9 C C doub N Y
43 C14 C13 C C sing N Y
44 C9 C8 C C sing N N
45 C9 C10 C C sing N Y
46 C8 H81 C H sing N N
47 C8 H82 C H sing N N
48 C13 O4 C O sing N N
49 C13 C12 C C doub N Y
50 O4 HO4 O H sing N N
51 C12 C11 C C sing N Y
52 C12 H12 C H sing N N
53 C11 C10 C C doub N Y
54 C11 H11 C H sing N N
55 C10 N7 C N sing N N
56 N7 CN7 N C sing N N
57 N7 C71 N C sing N N
58 CN7 HN71 C H sing N N
59 CN7 HN72 C H sing N N
60 CN7 HN73 C H sing N N
61 C71 H711 C H sing N N
62 C71 H712 C H sing N N
63 C71 H713 C H sing N N



MIY : Used in PDB Entries

Total Number of PDB Entries: 18
Ligand Code PDB Entry ID Type Total Distinct
MIY 2drd Open in New Window Bound ligand 1 1
MIY 2wq5 Open in New Window Bound ligand 1 1
MIY 2xpv Open in New Window Bound ligand 1 1
MIY 3aod Open in New Window Bound ligand 1 1
MIY 3v3n Open in New Window Bound ligand 4 1
MIY 4a99 Open in New Window Bound ligand 8 1
MIY 4ac0 Open in New Window Bound ligand 1 1
MIY 4dx5 Open in New Window Bound ligand 1 1
MIY 4u8v Open in New Window Bound ligand 1 1
MIY 4u8y Open in New Window Bound ligand 1 1
MIY 4u95 Open in New Window Bound ligand 1 1
MIY 5ent Open in New Window Bound ligand 1 1
MIY 6qjx Open in New Window Bound ligand 1 1
MIY 6rbm Open in New Window Bound ligand 1 1
MIY 6rxb Open in New Window Bound ligand 4 1
MIY 6zo6 Open in New Window Bound ligand 1 1
MIY 6zo8 Open in New Window Bound ligand 1 1
MIY 6zog Open in New Window Bound ligand 1 1