Chemical Components in the PDB

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YKS : Summary

Code

YKS

One-letter code

X

Molecule name

(1R,2S)-2-((S)-2-((((S)-1-(4,4-difluorocyclohexyl)-2-phenylethoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (1R,2S)-2-[(N-{[(1S)-1-(4,4-difluorocyclohexyl)-2-phenylethoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
OpenEye OEToolkits 2.0.7 (2~{S})-2-[[(2~{S})-2-[[(1~{S})-1-[4,4-bis(fluoranyl)cyclohexyl]-2-phenyl-ethoxy]carbonylamino]-4-methyl-pentanoyl]amino]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propane-1-sulfonic acid

Formula

C28 H41 F2 N3 O8 S

Formal charge

0

Molecular weight

617.702 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 CC(C)CC(NC(=O)OC(Cc1ccccc1)C1CCC(F)(F)CC1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O
SMILES CACTVS 3.385 CC(C)C[CH](NC(=O)O[CH](Cc1ccccc1)C2CCC(F)(F)CC2)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)[S](O)(=O)=O
SMILES OpenEye OEToolkits 2.0.7 CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OC(Cc2ccccc2)C3CCC(CC3)(F)F
Canonical SMILES CACTVS 3.385 CC(C)C[C@H](NC(=O)O[C@@H](Cc1ccccc1)C2CCC(F)(F)CC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)[S](O)(=O)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)O[C@@H](Cc2ccccc2)C3CCC(CC3)(F)F

IUPAC InChI

InChI=1S/C28H41F2N3O8S/c1-17(2)14-21(25(35)32-22(26(36)42(38,39)40)16-20-10-13-31-24(20)34)33-27(37)41-23(15-18-6-4-3-5-7-18)19-8-11-28(29,30)12-9-19/h3-7,17,19-23,26,36H,8-16H2,1-2H3,(H,31,34)(H,32,35)(H,33,37)(H,38,39,40)/t20-,21-,22-,23-,26+/m0/s1

IUPAC InChI key

PDAAZWNVPCMYBL-NRAAZAKSSA-N
YKS

wwPDB Information

Atom count

83 (42 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-03-11

Last modified at

2024-09-27

Status

Released

Obsoleted

Not Assigned



YKS : Atoms of Molecule

Total Number of Atoms: 83
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C11 C C1 S N N 0 3.645 0.588 -0.026
2 C12 C C2 N N N 0 4.598 0.365 1.149
3 C13 C C3 S N N 0 3.856 0.62 2.463
4 C14 C C4 N N N 0 4.778 0.402 3.642
5 C17 C C5 N N N 0 3.446 2.107 2.573
6 C19 C C6 R N N 0 4.423 0.493 -1.34
7 C23 C C7 S N N 0 -3.775 1.319 0.208
8 C02 C C8 N N N 0 -1.784 0.068 -0.198
9 C04 C C9 S N N 0 0.284 -1.197 -0.443
10 C05 C C10 N N N 0 0.722 -2.395 -1.289
11 C06 C C11 N N N 0 -0.308 -3.518 -1.155
12 C07 C C12 N N N 0 -1.628 -3.078 -1.794
13 C08 C C13 N N N 0 0.209 -4.771 -1.864
14 C09 C C14 N N N 0 1.362 -0.145 -0.465
15 C16 C C15 N N N 0 3.635 2.376 4.082
16 C24 C C16 N N N 0 -4.447 2.429 -0.603
17 C25 C C17 N Y N 0 -3.394 3.353 -1.158
18 C26 C C18 N Y N 0 -2.98 4.449 -0.425
19 C27 C C19 N Y N 0 -2.014 5.297 -0.935
20 C28 C C20 N Y N 0 -1.462 5.048 -2.177
21 C29 C C21 N Y N 0 -1.875 3.951 -2.91
22 C30 C C22 N Y N 0 -2.838 3.101 -2.399
23 C31 C C23 N N N 0 -4.847 0.454 0.874
24 C32 C C24 N N N 0 -4.179 -0.561 1.803
25 C33 C C25 N N N 0 -5.251 -1.426 2.47
26 C34 C C26 N N N 0 -6.049 -2.166 1.395
27 C37 C C27 N N N 0 -6.718 -1.151 0.466
28 C38 C C28 N N N 0 -5.646 -0.286 -0.2
29 F35 F F1 N N N 0 -7.029 -2.957 2.004
30 F36 F F2 N N N 0 -5.188 -2.981 0.653
31 O01 O O1 N N N 0 -1.463 0.32 0.946
32 N03 N N1 N N N 0 -0.954 -0.639 -0.991
33 N10 N N2 N N N 0 2.596 -0.435 -0.005
34 N15 N N3 N N N 0 4.638 1.402 4.53
35 O18 O O2 N N N 0 5.534 -0.538 3.769
36 O20 O O3 N N N 0 3.558 0.815 -2.431
37 O21 O O4 N N N 0 1.121 0.962 -0.896
38 O22 O O5 N N N 0 -2.969 0.495 -0.674
39 H1 H H1 N N N 0 3.191 1.576 0.056
40 H2 H H2 N N N 0 4.963 -0.662 1.132
41 H3 H H3 N N N 0 5.441 1.052 1.069
42 H4 H H4 N N N 0 2.98 -0.024 2.537
43 H5 H H5 N N N 0 4.105 2.739 1.978
44 H6 H H6 N N N 0 2.405 2.247 2.279
45 S1 S S1 N N Y 0 5.055 -1.195 -1.547
46 H8 H H8 N N N 0 5.258 1.193 -1.319
47 H9 H H9 N N N 0 -3.139 1.763 0.974
48 H10 H H10 N N N 0 0.113 -1.521 0.584
49 H11 H H11 N N N 0 0.797 -2.093 -2.334
50 H12 H H12 N N N 0 1.693 -2.749 -0.942
51 H13 H H13 N N N 0 -0.471 -3.738 -0.1
52 H14 H H14 N N N 0 -2.323 -3.917 -1.803
53 H15 H H15 N N N 0 -2.055 -2.258 -1.217
54 H16 H H16 N N N 0 -1.444 -2.747 -2.816
55 H17 H H17 N N N 0 1.149 -5.084 -1.409
56 H18 H H18 N N N 0 -0.525 -5.571 -1.769
57 H19 H H19 N N N 0 0.371 -4.551 -2.919
58 H20 H H20 N N N 0 3.998 3.391 4.242
59 H21 H H21 N N N 0 2.696 2.224 4.613
60 H22 H H22 N N N 0 -5.013 1.988 -1.423
61 H23 H H23 N N N 0 -5.122 2.993 0.042
62 H24 H H24 N N N 0 -3.411 4.644 0.546
63 H25 H H25 N N N 0 -1.691 6.154 -0.362
64 H26 H H26 N N N 0 -0.707 5.71 -2.575
65 H27 H H27 N N N 0 -1.444 3.756 -3.881
66 H31 H H31 N N N 0 -3.61 -0.034 2.569
67 H28 H H28 N N N 0 -3.158 2.242 -2.969
68 H29 H H29 N N N 0 -5.518 1.089 1.453
69 H30 H H30 N N N 0 -3.508 -1.196 1.225
70 H32 H H32 N N N 0 -4.774 -2.149 3.132
71 H33 H H33 N N N 0 -5.922 -0.791 3.048
72 H34 H H34 N N N 0 -7.287 -1.679 -0.299
73 H35 H H35 N N N 0 -7.389 -0.516 1.045
74 H36 H H36 N N N 0 -6.122 0.437 -0.862
75 H37 H H37 N N N 0 -4.975 -0.921 -0.779
76 H38 H H38 N N N 0 -1.177 -0.778 -1.925
77 H39 H H39 N N N 0 2.789 -1.321 0.34
78 H40 H H40 N N N 0 5.135 1.47 5.36
79 H41 H H41 N N N 0 2.792 0.231 -2.511
80 O1 O O6 N N Y 0 6.063 -1.472 -0.585
81 O2 O O7 N N Y 0 3.986 -2.104 -1.771
82 O3 O O8 N N Y 0 5.801 -1.161 -2.873
83 H7 H H7 N N Y 0 6.2 -2.006 -3.122



YKS : Chemical Bonds

Total Number of Bonds: 85
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 F36 C34 F C sing 1.4 N N
2 O18 C14 O C doub 1.21 N N
3 C34 F35 C F sing 1.4 N N
4 C34 C33 C C sing 1.53 N N
5 C34 C37 C C sing 1.53 N N
6 C32 C33 C C sing 1.53 N N
7 C32 C31 C C sing 1.53 N N
8 C14 N15 C N sing 1.34 N N
9 C14 C13 C C sing 1.51 N N
10 N15 C16 N C sing 1.47 N N
11 C37 C38 C C sing 1.53 N N
12 C38 C31 C C sing 1.53 N N
13 C31 C23 C C sing 1.53 N N
14 C23 C24 C C sing 1.53 N N
15 C23 O22 C O sing 1.45 N N
16 O01 C02 O C doub 1.21 N N
17 C24 C25 C C sing 1.51 N N
18 C13 C12 C C sing 1.53 N N
19 C13 C17 C C sing 1.55 N N
20 O22 C02 O C sing 1.35 N N
21 C02 N03 C N sing 1.35 N N
22 C16 C17 C C sing 1.54 N N
23 C12 C11 C C sing 1.53 N N
24 C07 C06 C C sing 1.53 N N
25 N03 C04 N C sing 1.46 N N
26 C04 C09 C C sing 1.51 N N
27 C04 C05 C C sing 1.53 N N
28 C25 C30 C C doub 1.38 N Y
29 C25 C26 C C sing 1.38 N Y
30 N10 C09 N C sing 1.35 N N
31 N10 C11 N C sing 1.47 N N
32 C30 C29 C C sing 1.38 N Y
33 C09 O21 C O doub 1.21 N N
34 C11 C19 C C sing 1.53 N N
35 C06 C05 C C sing 1.53 N N
36 C06 C08 C C sing 1.53 N N
37 C19 O20 C O sing 1.43 N N
38 C26 C27 C C doub 1.38 N Y
39 C29 C28 C C doub 1.38 N Y
40 C27 C28 C C sing 1.38 N Y
41 C11 H1 C H sing 1.09 N N
42 C12 H2 C H sing 1.09 N N
43 C12 H3 C H sing 1.09 N N
44 C13 H4 C H sing 1.09 N N
45 C17 H5 C H sing 1.09 N N
46 C17 H6 C H sing 1.09 N N
47 C19 S1 C S sing 1.81 N N
48 C19 H8 C H sing 1.09 N N
49 C23 H9 C H sing 1.09 N N
50 C04 H10 C H sing 1.09 N N
51 C05 H11 C H sing 1.09 N N
52 C05 H12 C H sing 1.09 N N
53 C06 H13 C H sing 1.09 N N
54 C07 H14 C H sing 1.09 N N
55 C07 H15 C H sing 1.09 N N
56 C07 H16 C H sing 1.09 N N
57 C08 H17 C H sing 1.09 N N
58 C08 H18 C H sing 1.09 N N
59 C08 H19 C H sing 1.09 N N
60 C16 H20 C H sing 1.09 N N
61 C16 H21 C H sing 1.09 N N
62 C24 H22 C H sing 1.09 N N
63 C24 H23 C H sing 1.09 N N
64 C26 H24 C H sing 1.08 N N
65 C27 H25 C H sing 1.08 N N
66 C28 H26 C H sing 1.08 N N
67 C29 H27 C H sing 1.08 N N
68 C30 H28 C H sing 1.08 N N
69 C31 H29 C H sing 1.09 N N
70 C32 H30 C H sing 1.09 N N
71 C32 H31 C H sing 1.09 N N
72 C33 H32 C H sing 1.09 N N
73 C33 H33 C H sing 1.09 N N
74 C37 H34 C H sing 1.09 N N
75 C37 H35 C H sing 1.09 N N
76 C38 H36 C H sing 1.09 N N
77 C38 H37 C H sing 1.09 N N
78 N03 H38 N H sing 0.97 N N
79 N10 H39 N H sing 0.97 N N
80 N15 H40 N H sing 0.97 N N
81 O20 H41 O H sing 0.97 N N
82 S1 O1 S O doub 1.42 N N
83 S1 O2 S O doub 1.42 N N
84 S1 O3 S O sing 1.52 N N
85 O3 H7 O H sing 0.97 N N



YKS : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
YKS 7m01 Open in New Window Bound ligand 2 1