Chemical Components in the PDB

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K0T : Summary

Code

K0T

One-letter code

X

Molecule name

(2~{S})-5-carbamimidamido-2-[[(2~{S})-2-[[(2~{S})-1-[5-(dimethylamino)naphthalen-1-yl]sulfonylpiperidin-2-yl]carbonylamino]-4-phenyl-butanoyl]amino]pentanoic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (2~{S})-5-carbamimidamido-2-[[(2~{S})-2-[[(2~{S})-1-[5-(dimethylamino)naphthalen-1-yl]sulfonylpiperidin-2-yl]carbonylamino]-4-phenyl-butanoyl]amino]pentanoic acid

Formula

C34 H45 N7 O6 S

Formal charge

0

Molecular weight

679.829 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN(C)c1cccc2c1cccc2[S](=O)(=O)N3CCCC[CH]3C(=O)N[CH](CCc4ccccc4)C(=O)N[CH](CCCNC(N)=N)C(O)=O
SMILES OpenEye OEToolkits 2.0.7 CN(C)c1cccc2c1cccc2S(=O)(=O)N3CCCCC3C(=O)NC(CCc4ccccc4)C(=O)NC(CCCNC(=N)N)C(=O)O
Canonical SMILES CACTVS 3.385 CN(C)c1cccc2c1cccc2[S](=O)(=O)N3CCCC[C@H]3C(=O)N[C@@H](CCc4ccccc4)C(=O)N[C@@H](CCCNC(N)=N)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 [H]/N=C(/N)\NCCC[C@@H](C(=O)O)NC(=O)[C@H](CCc1ccccc1)NC(=O)[C@@H]2CCCCN2S(=O)(=O)c3cccc4c3cccc4N(C)C

IUPAC InChI

InChI=1S/C34H45N7O6S/c1-40(2)28-17-8-14-25-24(28)13-9-18-30(25)48(46,47)41-22-7-6-16-29(41)32(43)38-26(20-19-23-11-4-3-5-12-23)31(42)39-27(33(44)45)15-10-21-37-34(35)36/h3-5,8-9,11-14,17-18,26-27,29H,6-7,10,15-16,19-22H2,1-2H3,(H,38,43)(H,39,42)(H,44,45)(H4,35,36,37)/t26-,27-,29-/m0/s1

IUPAC InChI key

MKNCAFDCRIGOAN-YCVJPRETSA-N
K0T

wwPDB Information

Atom count

93 (48 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-04-12

Last modified at

2020-05-08

Status

Released

Obsoleted

Not Assigned



K0T : Atoms of Molecule

Total Number of Atoms: 93
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O3 O O1 N N N 0 -2.182 -0.655 2.256
2 C4 C C1 N Y N 0 3.503 2.417 -1.856
3 C5 C C2 N Y N 0 2.18 2.2 -1.616
4 O4 O O2 N N N 0 -5.242 -1.842 1.734
5 C6 C C3 N Y N 0 1.76 1.52 -0.476
6 N1 N N1 N N N 0 2.681 -1.355 1.766
7 C7 C C4 N Y N 0 2.661 1.052 0.432
8 C8 C C5 N Y N 0 4.035 1.257 0.218
9 N2 N N2 N N N 0 -0.266 -1.634 0.757
10 C9 C C6 N Y N 0 4.992 0.788 1.134
11 O5 O O3 N N N 0 -6.38 -0.493 3.064
12 C10 C C7 N Y N 0 6.317 1.001 0.902
13 C11 C C8 N Y N 0 6.747 1.68 -0.235
14 C12 C C9 N N N 0 3.771 -1.809 2.642
15 N3 N N3 N N N 0 -3.616 -0.089 0.661
16 C13 C C10 N N N 0 3.326 -3.086 3.361
17 C14 C C11 N N N 0 2.879 -4.121 2.326
18 C15 C C12 N N N 0 1.689 -3.572 1.534
19 N4 N N4 N N N 0 -4.727 4.886 -0.465
20 N N N5 N N N 0 6.281 2.834 -2.291
21 C C C13 N N N 0 6.955 4.087 -1.926
22 O O O4 N N N 0 0.692 0.106 1.762
23 C1 C C14 N N N 0 7.159 1.982 -3.105
24 S S S1 N N N 0 2.107 0.195 1.868
25 O1 O O5 N N N 0 2.767 0.795 2.974
26 C16 C C15 S N N 0 2.116 -2.301 0.794
27 C17 C C16 N N N 0 0.921 -1.678 0.12
28 C18 C C17 S N N 0 -1.452 -1.127 0.062
29 C19 C C18 N N N 0 -2.093 -2.259 -0.744
30 C2 C C19 N Y N 0 5.84 2.156 -1.157
31 C20 C C20 N N N 0 -1.135 -2.703 -1.85
32 C21 C C21 N Y N 0 -1.766 -3.817 -2.645
33 C22 C C22 N Y N 0 -1.575 -5.132 -2.263
34 C23 C C23 N Y N 0 -2.154 -6.154 -2.991
35 C24 C C24 N Y N 0 -2.924 -5.862 -4.101
36 C25 C C25 N Y N 0 -3.115 -4.547 -4.483
37 C26 C C26 N Y N 0 -2.541 -3.524 -3.751
38 C27 C C27 N N N 0 -2.442 -0.607 1.073
39 C28 C C28 S N N 0 -4.578 0.417 1.643
40 C29 C C29 N N N 0 -5.476 1.465 0.984
41 C3 C C30 N Y N 0 4.46 1.944 -0.945
42 C30 C C31 N N N 0 -4.635 2.678 0.58
43 C31 C C32 N N N 0 -5.533 3.726 -0.079
44 C32 C C33 N N N 0 -5.322 5.963 -1.08
45 C33 C C34 N N N 0 -5.424 -0.722 2.15
46 H2 H H2 N N N 0 1.446 2.562 -2.321
47 N5 N N6 N N N 0 -6.673 5.95 -1.332
48 N6 N N7 N N N 0 -4.605 6.996 -1.423
49 O2 O O6 N N N 0 1.027 -1.216 -0.997
50 H1 H H1 N N N 0 3.814 2.947 -2.744
51 H3 H H3 N N N 0 0.705 1.361 -0.309
52 H4 H H4 N N N 0 -0.334 -1.938 1.676
53 H5 H H5 N N N 0 4.677 0.26 2.022
54 H6 H H6 N N N 0 -6.897 -1.256 3.359
55 H7 H H7 N N N 0 7.045 0.637 1.611
56 H8 H H8 N N N 0 7.804 1.835 -0.395
57 H9 H H9 N N N 0 4.658 -2.016 2.044
58 H10 H H10 N N N 0 3.997 -1.034 3.375
59 H11 H H11 N N N 0 -3.824 -0.051 -0.286
60 H12 H H12 N N N 0 4.158 -3.486 3.94
61 H13 H H13 N N N 0 2.495 -2.857 4.028
62 H14 H H14 N N N 0 3.703 -4.331 1.644
63 H15 H H15 N N N 0 2.585 -5.039 2.834
64 H16 H H16 N N N 0 1.357 -4.319 0.813
65 H17 H H17 N N N 0 0.874 -3.339 2.219
66 H18 H H18 N N N 0 -3.773 4.896 -0.287
67 H19 H H19 N N N 0 7.29 4.597 -2.83
68 H20 H H20 N N N 0 6.26 4.729 -1.384
69 H21 H H21 N N N 0 7.815 3.867 -1.294
70 H22 H H22 N N N 0 8.06 1.743 -2.54
71 H23 H H23 N N N 0 6.636 1.061 -3.362
72 H24 H H24 N N N 0 7.432 2.511 -4.019
73 H25 H H25 N N N 0 2.87 -2.552 0.048
74 H26 H H26 N N N 0 -1.162 -0.321 -0.611
75 H27 H H27 N N N 0 -2.302 -3.101 -0.084
76 H28 H H28 N N N 0 -3.023 -1.906 -1.189
77 H29 H H29 N N N 0 -0.925 -1.86 -2.51
78 H30 H H30 N N N 0 -0.204 -3.056 -1.406
79 H31 H H31 N N N 0 -0.973 -5.361 -1.395
80 H32 H H32 N N N 0 -2.004 -7.182 -2.693
81 H33 H H33 N N N 0 -3.375 -6.661 -4.671
82 H34 H H34 N N N 0 -3.717 -4.319 -5.35
83 H35 H H35 N N N 0 -2.693 -2.497 -4.047
84 H36 H H36 N N N 0 -4.042 0.871 2.477
85 H37 H H37 N N N 0 -5.944 1.037 0.097
86 H38 H H38 N N N 0 -6.248 1.777 1.687
87 H39 H H39 N N N 0 -4.167 3.106 1.467
88 H40 H H40 N N N 0 -3.863 2.366 -0.123
89 H41 H H41 N N N 0 -6.305 4.037 0.625
90 H42 H H42 N N N 0 -6.001 3.297 -0.965
91 H45 H H45 N N N 0 -5.024 7.755 -1.857
92 H43 H H43 N N N 0 -7.207 5.181 -1.076
93 H44 H H44 N N N 0 -7.093 6.709 -1.765



K0T : Chemical Bonds

Total Number of Bonds: 96
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C23 C22 C C doub 1.38 N Y
2 C23 C24 C C sing 1.38 N Y
3 C22 C21 C C sing 1.38 N Y
4 C13 C14 C C sing 1.53 N N
5 C13 C12 C C sing 1.53 N N
6 C24 C25 C C doub 1.38 N Y
7 C21 C20 C C sing 1.51 N N
8 C21 C26 C C doub 1.38 N Y
9 C14 C15 C C sing 1.53 N N
10 C20 C19 C C sing 1.53 N N
11 C12 N1 C N sing 1.47 N N
12 C25 C26 C C sing 1.38 N Y
13 C15 C16 C C sing 1.53 N N
14 C19 C18 C C sing 1.53 N N
15 O2 C17 O C doub 1.21 N N
16 C18 N2 C N sing 1.47 N N
17 C18 C27 C C sing 1.51 N N
18 N6 C32 N C doub 1.3 N N
19 C17 N2 C N sing 1.35 N N
20 C17 C16 C C sing 1.51 N N
21 N1 C16 N C sing 1.47 N N
22 N1 S N S sing 1.66 N N
23 C10 C9 C C doub 1.36 N Y
24 C10 C11 C C sing 1.39 N Y
25 N3 C27 N C sing 1.35 N N
26 N3 C28 N C sing 1.46 N N
27 O4 C33 O C doub 1.21 N N
28 C9 C8 C C sing 1.41 N Y
29 C29 C28 C C sing 1.53 N N
30 C29 C30 C C sing 1.53 N N
31 C31 N4 C N sing 1.46 N N
32 C31 C30 C C sing 1.53 N N
33 O S O S doub 1.42 N N
34 C27 O3 C O doub 1.21 N N
35 C32 N4 C N sing 1.38 N N
36 C32 N5 C N sing 1.37 N N
37 C11 C2 C C doub 1.38 N Y
38 S O1 S O doub 1.42 N N
39 S C7 S C sing 1.76 N N
40 C28 C33 C C sing 1.51 N N
41 C33 O5 C O sing 1.34 N N
42 C8 C7 C C doub 1.41 N Y
43 C8 C3 C C sing 1.42 N Y
44 C2 C3 C C sing 1.41 N Y
45 C2 N C N sing 1.39 N N
46 C7 C6 C C sing 1.36 N Y
47 C N C N sing 1.47 N N
48 C3 C4 C C doub 1.4 N Y
49 N C1 N C sing 1.47 N N
50 C6 C5 C C doub 1.39 N Y
51 C4 C5 C C sing 1.36 N Y
52 C4 H1 C H sing 1.08 N N
53 C5 H2 C H sing 1.08 N N
54 C6 H3 C H sing 1.08 N N
55 N2 H4 N H sing 0.97 N N
56 C9 H5 C H sing 1.08 N N
57 O5 H6 O H sing 0.97 N N
58 C10 H7 C H sing 1.08 N N
59 C11 H8 C H sing 1.08 N N
60 C12 H9 C H sing 1.09 N N
61 C12 H10 C H sing 1.09 N N
62 N3 H11 N H sing 0.97 N N
63 C13 H12 C H sing 1.09 N N
64 C13 H13 C H sing 1.09 N N
65 C14 H14 C H sing 1.09 N N
66 C14 H15 C H sing 1.09 N N
67 C15 H16 C H sing 1.09 N N
68 C15 H17 C H sing 1.09 N N
69 N4 H18 N H sing 0.97 N N
70 C H19 C H sing 1.09 N N
71 C H20 C H sing 1.09 N N
72 C H21 C H sing 1.09 N N
73 C1 H22 C H sing 1.09 N N
74 C1 H23 C H sing 1.09 N N
75 C1 H24 C H sing 1.09 N N
76 C16 H25 C H sing 1.09 N N
77 C18 H26 C H sing 1.09 N N
78 C19 H27 C H sing 1.09 N N
79 C19 H28 C H sing 1.09 N N
80 C20 H29 C H sing 1.09 N N
81 C20 H30 C H sing 1.09 N N
82 C22 H31 C H sing 1.08 N N
83 C23 H32 C H sing 1.08 N N
84 C24 H33 C H sing 1.08 N N
85 C25 H34 C H sing 1.08 N N
86 C26 H35 C H sing 1.08 N N
87 C28 H36 C H sing 1.09 N N
88 C29 H37 C H sing 1.09 N N
89 C29 H38 C H sing 1.09 N N
90 C30 H39 C H sing 1.09 N N
91 C30 H40 C H sing 1.09 N N
92 C31 H41 C H sing 1.09 N N
93 C31 H42 C H sing 1.09 N N
94 N5 H43 N H sing 0.97 N N
95 N5 H44 N H sing 0.97 N N
96 N6 H45 N H sing 0.97 N N



K0T : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
K0T 6rcy Open in New Window Bound ligand 1 1