Chemical Components in the PDB

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58K : Summary

Code

58K

One-letter code

X

Molecule name

cyclopeptin

Systematic names

ProgramVersionName
ACDLabs 12.01 (3S)-3-benzyl-4-methyl-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione
OpenEye OEToolkits 1.9.2 (3S)-4-methyl-3-(phenylmethyl)-1,3-dihydro-1,4-benzodiazepine-2,5-dione

Formula

C17 H16 N2 O2

Formal charge

0

Molecular weight

280.321 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C2(N(C(Cc1ccccc1)C(=O)Nc3c2cccc3)C)=O
SMILES CACTVS 3.385 CN1[CH](Cc2ccccc2)C(=O)Nc3ccccc3C1=O
SMILES OpenEye OEToolkits 1.9.2 CN1C(C(=O)Nc2ccccc2C1=O)Cc3ccccc3
Canonical SMILES CACTVS 3.385 CN1[C@@H](Cc2ccccc2)C(=O)Nc3ccccc3C1=O
Canonical SMILES OpenEye OEToolkits 1.9.2 CN1[C@H](C(=O)Nc2ccccc2C1=O)Cc3ccccc3

IUPAC InChI

InChI=1S/C17H16N2O2/c1-19-15(11-12-7-3-2-4-8-12)16(20)18-14-10-6-5-9-13(14)17(19)21/h2-10,15H,11H2,1H3,(H,18,20)/t15-/m0/s1

IUPAC InChI key

KSQNKZMAMGACTL-HNNXBMFYSA-N
58K

wwPDB Information

Atom count

37 (21 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-08-20

Last modified at

2015-11-20

Status

Released

Obsoleted

Not Assigned



58K : Atoms of Molecule

Total Number of Atoms: 37
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N N N 0 -0.733 0.038 -1.514
2 C7 C C2 S N N 0 0.215 -1.525 0.101
3 C8 C C3 N N N 0 0.551 -0.42 1.104
4 C10 C C4 N Y N 0 3.037 -0.427 1.396
5 C13 C C5 N Y N 0 3.315 1.712 -0.333
6 C15 C C6 N N N 0 -1.104 -2.151 0.464
7 C20 C C7 N Y N 0 -3.25 2.0 1.295
8 C12 C C8 N Y N 0 4.432 1.15 0.255
9 C11 C C9 N Y N 0 4.293 0.08 1.12
10 C14 C C10 N Y N 0 2.06 1.198 -0.066
11 C9 C C11 N Y N 0 1.92 0.132 0.803
12 O16 O O1 N N N 0 -1.155 -3.349 0.651
13 N17 N N1 N N N 0 -2.215 -1.431 0.585
14 C18 C C12 N Y N 0 -2.295 -0.049 0.457
15 C19 C C13 N Y N 0 -3.115 0.632 1.361
16 C1 C C14 N Y N 0 -2.583 2.718 0.305
17 C2 C C15 N Y N 0 -1.775 2.063 -0.594
18 C3 C C16 N Y N 0 -1.619 0.669 -0.529
19 O5 O O2 N N N 0 -0.771 0.452 -2.657
20 N6 N N2 N N N 0 0.114 -0.954 -1.242
21 C23 C C17 N N N 0 0.962 -1.485 -2.312
22 H1 H H1 N N N 0 0.998 -2.283 0.117
23 H2 H H2 N N N 0 -0.188 0.378 1.027
24 H3 H H3 N N N 0 0.538 -0.83 2.114
25 H4 H H4 N N N 0 2.928 -1.263 2.071
26 H5 H H5 N N N 0 3.422 2.554 -1.002
27 H6 H H6 N N N 0 -3.883 2.517 2.002
28 H7 H H7 N N N 0 5.412 1.551 0.047
29 H8 H H8 N N N 0 5.165 -0.359 1.58
30 H9 H H9 N N N 0 1.187 1.638 -0.526
31 H10 H H10 N N N 0 -3.036 -1.906 0.79
32 H11 H H11 N N N 0 -3.648 0.078 2.12
33 H12 H H12 N N N 0 -2.701 3.79 0.243
34 H13 H H13 N N N 0 -1.26 2.625 -1.36
35 H14 H H14 N N N 0 0.758 -0.948 -3.238
36 H15 H H15 N N N 0 2.01 -1.356 -2.041
37 H16 H H16 N N N 0 0.751 -2.545 -2.451



58K : Chemical Bonds

Total Number of Bonds: 39
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C19 C20 C C doub 1.38 N Y
2 C19 C18 C C sing 1.4 N Y
3 C20 C1 C C sing 1.39 N Y
4 N17 C18 N C sing 1.39 N N
5 N17 C15 N C sing 1.33 N N
6 C18 C3 C C doub 1.39 N Y
7 C1 C2 C C doub 1.37 N Y
8 O16 C15 O C doub 1.21 N N
9 C15 C7 C C sing 1.5 N N
10 C3 C2 C C sing 1.4 N Y
11 C3 C4 C C sing 1.47 N N
12 C7 C8 C C sing 1.53 N N
13 C7 N6 C N sing 1.46 N N
14 C4 N6 C N sing 1.33 N N
15 C4 O5 C O doub 1.22 N N
16 C8 C9 C C sing 1.51 N N
17 N6 C23 N C sing 1.46 N N
18 C9 C14 C C doub 1.38 N Y
19 C9 C10 C C sing 1.38 N Y
20 C14 C13 C C sing 1.38 N Y
21 C10 C11 C C doub 1.38 N Y
22 C13 C12 C C doub 1.38 N Y
23 C11 C12 C C sing 1.38 N Y
24 C7 H1 C H sing 1.09 N N
25 C8 H2 C H sing 1.09 N N
26 C8 H3 C H sing 1.09 N N
27 C10 H4 C H sing 1.08 N N
28 C13 H5 C H sing 1.08 N N
29 C20 H6 C H sing 1.08 N N
30 C12 H7 C H sing 1.08 N N
31 C11 H8 C H sing 1.08 N N
32 C14 H9 C H sing 1.08 N N
33 N17 H10 N H sing 0.97 N N
34 C19 H11 C H sing 1.08 N N
35 C1 H12 C H sing 1.08 N N
36 C2 H13 C H sing 1.08 N N
37 C23 H14 C H sing 1.09 N N
38 C23 H15 C H sing 1.09 N N
39 C23 H16 C H sing 1.09 N N



58K : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
58K 5daw Open in New Window Bound ligand 1 1
58K 5oa7 Open in New Window Bound ligand 1 1
58K 5y7r Open in New Window Bound ligand 1 1
58K 6eoz Open in New Window Bound ligand 1 1