Chemical Components in the PDB

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YV6 : Summary

Code

YV6

One-letter code

X

Molecule name

methyl (3S)-1-[N-(4-sulfanylbutanoyl)-L-valyl-3-hydroxy-L-phenylalanyl]-1,2-diazinane-3-carboxylate

Systematic names

ProgramVersionName
ACDLabs 12.01 methyl (3S)-1-[N-(4-sulfanylbutanoyl)-L-valyl-3-hydroxy-L-phenylalanyl]-1,2-diazinane-3-carboxylate
OpenEye OEToolkits 2.0.7 methyl (3~{S})-1-[(2~{S})-3-(3-hydroxyphenyl)-2-[[(2~{S})-3-methyl-2-(4-sulfanylbutanoylamino)butanoyl]amino]propanoyl]-1,2-diazinane-3-carboxylate

Formula

C24 H36 N4 O6 S

Formal charge

0

Molecular weight

508.631 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(N1CCCC(N1)C(=O)OC)C(Cc1cccc(O)c1)NC(=O)C(NC(=O)CCCS)C(C)C
SMILES CACTVS 3.385 COC(=O)[CH]1CCCN(N1)C(=O)[CH](Cc2cccc(O)c2)NC(=O)[CH](NC(=O)CCCS)C(C)C
SMILES OpenEye OEToolkits 2.0.7 CC(C)C(C(=O)NC(Cc1cccc(c1)O)C(=O)N2CCCC(N2)C(=O)OC)NC(=O)CCCS
Canonical SMILES CACTVS 3.385 COC(=O)[C@@H]1CCCN(N1)C(=O)[C@H](Cc2cccc(O)c2)NC(=O)[C@@H](NC(=O)CCCS)C(C)C
Canonical SMILES OpenEye OEToolkits 2.0.7 CC(C)[C@@H](C(=O)N[C@@H](Cc1cccc(c1)O)C(=O)N2CCC[C@H](N2)C(=O)OC)NC(=O)CCCS

IUPAC InChI

InChI=1S/C24H36N4O6S/c1-15(2)21(26-20(30)10-6-12-35)22(31)25-19(14-16-7-4-8-17(29)13-16)23(32)28-11-5-9-18(27-28)24(33)34-3/h4,7-8,13,15,18-19,21,27,29,35H,5-6,9-12,14H2,1-3H3,(H,25,31)(H,26,30)/t18-,19-,21-/m0/s1

IUPAC InChI key

VHGYJBMAJUGDAM-ZJOUEHCJSA-N
YV6

wwPDB Information

Atom count

71 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-02-22

Last modified at

2024-04-19

Status

Released

Obsoleted

Not Assigned



YV6 : Atoms of Molecule

Total Number of Atoms: 71
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -6.935 3.249 -0.231
2 C10 C C2 N Y N 0 -0.988 1.304 -0.551
3 C11 C C3 N Y N 0 0.223 1.43 -1.206
4 C12 C C4 N Y N 0 1.06 2.493 -0.919
5 C13 C C5 N Y N 0 0.687 3.432 0.023
6 C14 C C6 N Y N 0 -0.528 3.308 0.681
7 C15 C C7 N Y N 0 -1.365 2.241 0.392
8 C16 C C8 N N N 0 0.846 -0.926 0.345
9 C17 C C9 S N N 0 2.227 -1.49 0.135
10 C18 C C10 N N N 0 4.458 -0.528 -0.049
11 C19 C C11 N N N 0 5.486 0.51 0.323
12 C2 C C12 N N N 0 -5.85 1.143 0.027
13 C20 C C13 N N N 0 6.788 0.231 -0.432
14 C21 C C14 N N N 0 7.832 1.284 -0.054
15 C27 C C15 N N N 0 2.411 -2.729 1.014
16 C28 C C16 N N N 0 3.793 -3.334 0.76
17 C29 C C17 N N N 0 2.292 -2.331 2.487
18 C3 C C18 S N N 0 -5.32 -0.166 -0.5
19 C4 C C19 N N N 0 -6.474 -1.163 -0.643
20 C5 C C20 N N N 0 -5.927 -2.493 -1.171
21 C6 C C21 N N N 0 -4.85 -3.004 -0.207
22 C7 C C22 N N N 0 -2.56 -2.142 -0.185
23 C8 C C23 S N N 0 -1.571 -1.03 0.049
24 C9 C C24 N N N 0 -1.9 0.147 -0.871
25 N1 N N1 N N N 0 -3.875 -1.928 0.018
26 N2 N N2 N N N 0 -4.323 -0.703 0.437
27 N3 N N3 N N N 0 -0.218 -1.512 -0.24
28 N4 N N4 N N N 0 3.227 -0.482 0.497
29 O1 O O1 N N N 0 -6.449 2.008 -0.807
30 O2 O O2 N N N 0 -5.735 1.414 1.198
31 O3 O O3 N N N 0 -2.174 -3.23 -0.557
32 O4 O O4 N N N 0 -0.897 4.23 1.609
33 O5 O O5 N N N 0 0.691 0.056 1.04
34 O6 O O6 N N N 0 4.739 -1.403 -0.84
35 S1 S S1 N N N 0 9.375 0.953 -0.948
36 H1 H H1 N N N 0 -7.672 3.027 0.541
37 H2 H H2 N N N 0 -6.101 3.796 0.209
38 H3 H H3 N N N 0 -7.396 3.855 -1.01
39 H4 H H4 N N N 0 0.516 0.697 -1.943
40 H5 H H5 N N N 0 2.006 2.589 -1.432
41 H6 H H6 N N N 0 1.341 4.262 0.247
42 H7 H H7 N N N 0 -2.311 2.142 0.903
43 H8 H H8 N N N 0 2.352 -1.766 -0.912
44 H9 H H9 N N N 0 5.116 1.5 0.056
45 H10 H H10 N N N 0 5.672 0.468 1.396
46 H11 H H11 N N N 0 7.157 -0.759 -0.165
47 H12 H H12 N N N 0 6.602 0.272 -1.505
48 H13 H H13 N N N 0 7.462 2.274 -0.321
49 H14 H H14 N N N 0 8.018 1.243 1.019
50 H15 H H15 N N N 0 1.643 -3.463 0.773
51 H16 H H16 N N N 0 4.562 -2.64 1.099
52 H17 H H17 N N N 0 3.884 -4.273 1.306
53 H18 H H18 N N N 0 3.917 -3.521 -0.307
54 H19 H H19 N N N 0 1.308 -1.9 2.668
55 H20 H H20 N N N 0 2.423 -3.213 3.113
56 H21 H H21 N N N 0 3.061 -1.597 2.728
57 H22 H H22 N N N 0 -4.856 -0.006 -1.472
58 H23 H H23 N N N 0 -6.941 -1.321 0.329
59 H24 H H24 N N N 0 -7.211 -0.768 -1.341
60 H25 H H25 N N N 0 -6.736 -3.221 -1.233
61 H26 H H26 N N N 0 -5.494 -2.343 -2.16
62 H27 H H27 N N N 0 -5.31 -3.285 0.74
63 H28 H H28 N N N 0 -4.347 -3.867 -0.643
64 H29 H H29 N N N 0 -1.627 -0.707 1.088
65 H30 H H30 N N N 0 -2.936 0.449 -0.718
66 H31 H H31 N N N 0 -1.757 -0.151 -1.909
67 H32 H H32 N N N 0 -4.697 -0.756 1.373
68 H33 H H33 N N N 0 -0.087 -2.253 -0.852
69 H34 H H34 N N N 0 3.002 0.219 1.129
70 H35 H H35 N N N 0 -1.394 4.976 1.247
71 H36 H H36 N N N 0 10.186 1.939 -0.526



YV6 : Chemical Bonds

Total Number of Bonds: 72
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C28 C27 C C sing 1.53 N N
2 C29 C27 C C sing 1.53 N N
3 C27 C17 C C sing 1.53 N N
4 O5 C16 O C doub 1.21 N N
5 C17 C16 C C sing 1.51 N N
6 C17 N4 C N sing 1.47 N N
7 C16 N3 C N sing 1.35 N N
8 N4 C18 N C sing 1.35 N N
9 O3 C7 O C doub 1.21 N N
10 N3 C8 N C sing 1.47 N N
11 C6 N1 C N sing 1.47 N N
12 C6 C5 C C sing 1.53 N N
13 C18 C19 C C sing 1.51 N N
14 C18 O6 C O doub 1.21 N N
15 C7 N1 C N sing 1.35 N N
16 C7 C8 C C sing 1.51 N N
17 N1 N2 N N sing 1.37 N N
18 C19 C20 C C sing 1.53 N N
19 C8 C9 C C sing 1.53 N N
20 N2 C3 N C sing 1.47 N N
21 C5 C4 C C sing 1.53 N N
22 O2 C2 O C doub 1.21 N N
23 C4 C3 C C sing 1.53 N N
24 C3 C2 C C sing 1.51 N N
25 O4 C14 O C sing 1.36 N N
26 C15 C14 C C doub 1.39 N Y
27 C15 C10 C C sing 1.38 N Y
28 C20 C21 C C sing 1.53 N N
29 C9 C10 C C sing 1.51 N N
30 C2 O1 C O sing 1.34 N N
31 C21 S1 C S sing 1.81 N N
32 C14 C13 C C sing 1.39 N Y
33 C10 C11 C C doub 1.38 N Y
34 C13 C12 C C doub 1.38 N Y
35 C11 C12 C C sing 1.38 N Y
36 O1 C1 O C sing 1.45 N N
37 C1 H1 C H sing 1.09 N N
38 C1 H2 C H sing 1.09 N N
39 C1 H3 C H sing 1.09 N N
40 C11 H4 C H sing 1.08 N N
41 C12 H5 C H sing 1.08 N N
42 C13 H6 C H sing 1.08 N N
43 C15 H7 C H sing 1.08 N N
44 C17 H8 C H sing 1.09 N N
45 C19 H9 C H sing 1.09 N N
46 C19 H10 C H sing 1.09 N N
47 C20 H11 C H sing 1.09 N N
48 C20 H12 C H sing 1.09 N N
49 C21 H13 C H sing 1.09 N N
50 C21 H14 C H sing 1.09 N N
51 C27 H15 C H sing 1.09 N N
52 C28 H16 C H sing 1.09 N N
53 C28 H17 C H sing 1.09 N N
54 C28 H18 C H sing 1.09 N N
55 C29 H19 C H sing 1.09 N N
56 C29 H20 C H sing 1.09 N N
57 C29 H21 C H sing 1.09 N N
58 C3 H22 C H sing 1.09 N N
59 C4 H23 C H sing 1.09 N N
60 C4 H24 C H sing 1.09 N N
61 C5 H25 C H sing 1.09 N N
62 C5 H26 C H sing 1.09 N N
63 C6 H27 C H sing 1.09 N N
64 C6 H28 C H sing 1.09 N N
65 C8 H29 C H sing 1.09 N N
66 C9 H30 C H sing 1.09 N N
67 C9 H31 C H sing 1.09 N N
68 N2 H32 N H sing 1.01 N N
69 N3 H33 N H sing 0.97 N N
70 N4 H34 N H sing 0.97 N N
71 O4 H35 O H sing 0.97 N N
72 S1 H36 S H sing 1.34 N N



YV6 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
YV6 8g9q Open in New Window Bound ligand 1 1