Chemical Components in the PDB

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9Z1 : Summary

Code

9Z1

One-letter code

X

Molecule name

(3E,7aR,12aS)-6-hydroxy-3-[(1H-imidazol-4-yl)methylidene]-12-methoxy-7a-(2-methylbut-3-en-2-yl)-7a,12-dihydro-1H,5H-imidazo[1',2':1,2]pyrido[2,3-b]indole-2,5(3H)-dione

Synonyms

Meleagrin

Systematic names

ProgramVersionName
ACDLabs 12.01 (3E,7aR,12aS)-6-hydroxy-3-[(1H-imidazol-4-yl)methylidene]-12-methoxy-7a-(2-methylbut-3-en-2-yl)-7a,12-dihydro-1H,5H-imidazo[1',2':1,2]pyrido[2,3-b]indole-2,5(3H)-dione

Formula

C23 H23 N5 O4

Formal charge

0

Molecular weight

433.46 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 CC(C)(C35C2(NC(\C(=C/c1cncn1)N2C(C(=C3)O)=O)=O)N(c4ccccc45)OC)/C=C
SMILES CACTVS 3.385 CON1c2ccccc2[C]3(C=C(O)C(=O)N4C(=Cc5c[nH]cn5)C(=O)N[C]134)C(C)(C)C=C
SMILES OpenEye OEToolkits 2.0.6 CC(C)(C=C)C12C=C(C(=O)N3C1(NC(=O)C3=Cc4c[nH]cn4)N(c5c2cccc5)OC)O
Canonical SMILES CACTVS 3.385 CON1c2ccccc2[C@@]3(C=C(O)C(=O)N4C(=C/c5c[nH]cn5)/C(=O)N[C@@]134)C(C)(C)C=C
Canonical SMILES OpenEye OEToolkits 2.0.6 CC(C)(C=C)[C@@]12C=C(C(=O)N\3[C@]1(NC(=O)/C3=C\c4c[nH]cn4)N(c5c2cccc5)OC)O

IUPAC InChI

InChI=1S/C23H23N5O4/c1-5-21(2,3)22-11-18(29)20(31)27-17(10-14-12-24-13-25-14)19(30)26-23(22,27)28(32-4)16-9-7-6-8-15(16)22/h5-13,29H,1H2,2-4H3,(H,24,25)(H,26,30)/b17-10+/t22-,23-/m0/s1

IUPAC InChI key

JTJJJLSLKZFEPJ-ZAYCRUKZSA-N
9Z1

wwPDB Information

Atom count

55 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-06-27

Last modified at

2018-06-22

Status

Released

Obsoleted

Not Assigned



9Z1 : Atoms of Molecule

Total Number of Atoms: 55
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C11 C C1 N N N 0 0.402 0.758 2.682
2 C10 C C2 N N N 0 0.415 3.193 1.539
3 C12 C C3 N N N 0 2.887 1.022 2.688
4 C16 C C4 N N N 0 0.19 -2.304 -2.727
5 C1 C C5 N Y N 0 2.279 0.156 -1.611
6 C13 C C6 S N N 0 0.471 0.051 -0.196
7 C18 C C7 N N N 0 -0.239 -2.064 0.895
8 C2 C C8 N Y N 0 3.047 0.387 -2.752
9 C20 C C9 N N N 0 1.178 -2.287 1.264
10 C22 C C10 N N N 0 2.061 -1.305 1.167
11 C23 C C11 N N N 0 -1.764 -0.257 0.147
12 C24 C C12 N N N 0 -2.978 -0.852 0.242
13 C25 C C13 N Y N 0 -4.188 -0.117 -0.149
14 C26 C C14 N Y N 0 -5.46 -0.617 -0.186
15 C28 C C15 N Y N 0 -5.484 1.488 -0.81
16 C3 C C16 N Y N 0 4.312 0.923 -2.565
17 C30 C C17 N N N 0 -1.51 1.155 -0.17
18 C4 C C18 N Y N 0 4.802 1.22 -1.31
19 C5 C C19 N Y N 0 4.047 0.993 -0.164
20 C6 C C20 N Y N 0 2.79 0.458 -0.342
21 C7 C C21 R N N 0 1.735 0.085 0.679
22 C8 C C22 N N N 0 1.625 1.092 1.826
23 C9 C C23 N N N 0 1.479 2.482 1.261
24 N14 N N1 N N N 0 0.988 -0.358 -1.518
25 N17 N N2 N N N 0 -0.524 -0.874 0.332
26 N27 N N3 N Y N 0 -6.268 0.398 -0.602
27 N29 N N4 N Y N 0 -4.248 1.183 -0.536
28 N32 N N5 N N N 0 -0.18 1.354 -0.299
29 O15 O O1 N N N 0 0.993 -1.815 -1.65
30 O19 O O2 N N N 0 -1.095 -2.906 1.088
31 O21 O O3 N N N 0 1.575 -3.51 1.706
32 O31 O O4 N N N 0 -2.365 2.012 -0.298
33 H1 H H1 N N N 0 0.371 1.423 3.546
34 H2 H H2 N N N 0 -0.503 0.89 2.089
35 H3 H H3 N N N 0 0.467 -0.276 3.021
36 H4 H H4 N N N 0 -0.358 2.784 2.173
37 H5 H H5 N N N 0 0.311 4.189 1.135
38 H6 H H6 N N N 0 3.182 -0.02 2.817
39 H7 H H7 N N N 0 3.692 1.57 2.2
40 H8 H H8 N N N 0 2.685 1.465 3.664
41 H9 H H9 N N N 0 0.247 -3.392 -2.758
42 H10 H H10 N N N 0 -0.845 -1.998 -2.576
43 H11 H H11 N N N 0 0.556 -1.894 -3.668
44 H12 H H12 N N N 0 2.673 0.158 -3.739
45 H13 H H13 N N N 0 3.08 -1.512 1.458
46 H14 H H14 N N N 0 -3.056 -1.865 0.606
47 H15 H H15 N N N 0 -5.765 -1.622 0.067
48 H16 H H16 N N N 0 -5.831 2.454 -1.146
49 H17 H H17 N N N 0 4.933 1.114 -3.428
50 H18 H H18 N N N 0 5.793 1.638 -1.215
51 H19 H H19 N N N 0 4.428 1.224 0.819
52 H20 H H20 N N N 0 2.252 2.891 0.627
53 H21 H H21 N N N 0 -7.228 0.351 -0.727
54 H23 H H23 N N N 0 0.262 2.207 -0.435
55 H24 H H24 N N N 0 0.864 -4.164 1.744



9Z1 : Chemical Bonds

Total Number of Bonds: 59
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O19 C18 O C doub 1.22 N N
2 O21 C20 O C sing 1.36 N N
3 C11 C8 C C sing 1.53 N N
4 C12 C8 C C sing 1.53 N N
5 C18 C20 C C sing 1.48 N N
6 C18 N17 C N sing 1.35 N N
7 C20 C22 C C doub 1.32 N N
8 C24 C25 C C sing 1.47 N N
9 C24 C23 C C doub 1.36 E N
10 C25 C26 C C doub 1.37 N Y
11 C25 N29 C N sing 1.36 N Y
12 C26 N27 C N sing 1.36 N Y
13 N29 C28 N C doub 1.3 N Y
14 N27 C28 N C sing 1.36 N Y
15 C8 C7 C C sing 1.53 N N
16 C8 C9 C C sing 1.51 N N
17 C22 C7 C C sing 1.51 N N
18 N17 C23 N C sing 1.4 N N
19 N17 C13 N C sing 1.46 N N
20 C23 C30 C C sing 1.47 N N
21 C7 C13 C C sing 1.54 N N
22 C7 C6 C C sing 1.51 N N
23 C9 C10 C C doub 1.31 N N
24 C13 N32 C N sing 1.46 N N
25 C13 N14 C N sing 1.48 N N
26 C30 O31 C O doub 1.22 N N
27 C30 N32 C N sing 1.35 N N
28 C6 C5 C C doub 1.38 N Y
29 C6 C1 C C sing 1.4 N Y
30 N14 O15 N O sing 1.46 N N
31 N14 C1 N C sing 1.39 N N
32 O15 C16 O C sing 1.43 N N
33 C5 C4 C C sing 1.39 N Y
34 C1 C2 C C doub 1.39 N Y
35 C4 C3 C C doub 1.38 N Y
36 C2 C3 C C sing 1.39 N Y
37 C11 H1 C H sing 1.09 N N
38 C11 H2 C H sing 1.09 N N
39 C11 H3 C H sing 1.09 N N
40 C10 H4 C H sing 1.08 N N
41 C10 H5 C H sing 1.08 N N
42 C12 H6 C H sing 1.09 N N
43 C12 H7 C H sing 1.09 N N
44 C12 H8 C H sing 1.09 N N
45 C16 H9 C H sing 1.09 N N
46 C16 H10 C H sing 1.09 N N
47 C16 H11 C H sing 1.09 N N
48 C2 H12 C H sing 1.08 N N
49 C22 H13 C H sing 1.08 N N
50 C24 H14 C H sing 1.08 N N
51 C26 H15 C H sing 1.08 N N
52 C28 H16 C H sing 1.08 N N
53 C3 H17 C H sing 1.08 N N
54 C4 H18 C H sing 1.08 N N
55 C5 H19 C H sing 1.08 N N
56 C9 H20 C H sing 1.08 N N
57 N27 H21 N H sing 0.97 N N
58 N32 H23 N H sing 0.97 N N
59 O21 H24 O H sing 0.97 N N



9Z1 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
9Z1 5w7s Open in New Window Bound ligand 1 1