Chemical Components in the PDB

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TFN : Summary

Code

TFN

One-letter code

X

Molecule name

N-(benzylsulfonyl)-O-tert-butyl-D-seryl-N-(4-carbamimidoylbenzyl)glycinamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-(benzylsulfonyl)-O-tert-butyl-D-seryl-N-(4-carbamimidoylbenzyl)glycinamide
OpenEye OEToolkits 1.7.6 (2R)-N-[2-[(4-carbamimidoylphenyl)methylamino]-2-oxidanylidene-ethyl]-3-[(2-methylpropan-2-yl)oxy]-2-[(phenylmethyl)sulfonylamino]propanamide

Formula

C24 H33 N5 O5 S

Formal charge

0

Molecular weight

503.614 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=S(=O)(NC(C(=O)NCC(=O)NCc1ccc(C(=[N@H])N)cc1)COC(C)(C)C)Cc2ccccc2
SMILES CACTVS 3.370 CC(C)(C)OC[CH](N[S](=O)(=O)Cc1ccccc1)C(=O)NCC(=O)NCc2ccc(cc2)C(N)=N
SMILES OpenEye OEToolkits 1.7.6 CC(C)(C)OCC(C(=O)NCC(=O)NCc1ccc(cc1)C(=N)N)NS(=O)(=O)Cc2ccccc2
Canonical SMILES CACTVS 3.370 CC(C)(C)OC[C@@H](N[S](=O)(=O)Cc1ccccc1)C(=O)NCC(=O)NCc2ccc(cc2)C(N)=N
Canonical SMILES OpenEye OEToolkits 1.7.6 [H]/N=C(/c1ccc(cc1)CNC(=O)CNC(=O)[C@@H](COC(C)(C)C)NS(=O)(=O)Cc2ccccc2)\N

IUPAC InChI

InChI=1S/C24H33N5O5S/c1-24(2,3)34-15-20(29-35(32,33)16-18-7-5-4-6-8-18)23(31)28-14-21(30)27-13-17-9-11-19(12-10-17)22(25)26/h4-12,20,29H,13-16H2,1-3H3,(H3,25,26)(H,27,30)(H,28,31)/t20-/m1/s1

IUPAC InChI key

NAEBSNBHOZLKPM-HXUWFJFHSA-N

Has sub-components

PMS , 3PM , GLY , 00S
TFN

wwPDB Information

Atom count

68 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

PEPTIDE-LIKE

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-11-18

Last modified at

2012-01-11

Status

Released

Obsoleted

Not Assigned



TFN : Atoms of Molecule

Total Number of Atoms: 68
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C7 C C7 N N N 0 -5.417 0.023 -0.17
2 S8 S S8 N N N 0 -4.56 1.118 0.996
3 C5 C C5 N Y N 0 -6.765 0.605 -0.507
4 C4 C C4 N Y N 0 -6.897 1.467 -1.58
5 C3 C C3 N Y N 0 -8.134 2.001 -1.889
6 C2 C C2 N Y N 0 -9.239 1.673 -1.127
7 C1 C C1 N Y N 0 -9.107 0.811 -0.054
8 C6 C C6 N Y N 0 -7.872 0.272 0.252
9 O35 O O35 N N N 0 -4.205 2.34 0.363
10 O34 O O34 N N N 0 -5.211 1.109 2.259
11 N9 N N9 N N N 0 -3.111 0.368 1.278
12 C10 C C10 R N N 0 -2.143 0.212 0.19
13 C11 C C11 N N N 0 -2.315 -1.167 -0.452
14 O12 O O12 N N N 0 -1.982 -2.18 0.499
15 C13 C C13 N N N 0 -2.11 -3.512 -0.002
16 C15 C C15 N N N 0 -1.18 -3.697 -1.203
17 C16 C C16 N N N 0 -1.73 -4.508 1.095
18 C14 C C14 N N N 0 -3.557 -3.757 -0.434
19 C17 C C17 N N N 0 -0.745 0.339 0.738
20 O18 O O18 N N N 0 -0.575 0.541 1.922
21 N19 N N19 N N N 0 0.315 0.229 -0.086
22 C20 C C20 N N N 0 1.674 0.353 0.447
23 C21 C C21 N N N 0 2.67 0.192 -0.673
24 O22 O O22 N N N 0 2.283 -0.007 -1.804
25 N23 N N23 N N N 0 3.991 0.269 -0.416
26 C24 C C24 N N N 0 4.959 0.112 -1.504
27 C25 C C25 N Y N 0 6.356 0.24 -0.955
28 C30 C C30 N Y N 0 7.026 -0.885 -0.507
29 C29 C C29 N Y N 0 8.306 -0.774 -0.003
30 C28 C C28 N Y N 0 8.924 0.475 0.053
31 C31 C C31 N N N 0 10.298 0.6 0.593
32 N32 N N32 N N N 0 10.931 -0.457 1.015
33 N33 N N33 N N N 0 10.906 1.835 0.647
34 C27 C C27 N Y N 0 8.245 1.605 -0.4
35 C26 C C26 N Y N 0 6.967 1.48 -0.907
36 H7 H H7 N N N 0 -4.825 -0.074 -1.08
37 H7A H H7A N N N 0 -5.549 -0.959 0.284
38 H4 H H4 N N N 0 -6.034 1.724 -2.176
39 H3 H H3 N N N 0 -8.237 2.675 -2.727
40 H2 H H2 N N N 0 -10.205 2.091 -1.368
41 H1 H H1 N N N 0 -9.971 0.555 0.542
42 H6 H H6 N N N 0 -7.769 -0.402 1.089
43 HN9 H HN9 N N N 0 -2.903 0.033 2.164
44 H10 H H10 N N N 0 -2.311 0.985 -0.56
45 H11 H H11 N N N 0 -3.35 -1.293 -0.77
46 H11A H H11A N N N 0 -1.657 -1.25 -1.317
47 H15 H H15 N N N 0 -0.149 -3.522 -0.895
48 H15A H H15A N N N 0 -1.278 -4.713 -1.585
49 H15B H H15B N N N 0 -1.451 -2.987 -1.985
50 H16 H H16 N N N 0 -2.392 -4.377 1.951
51 H16A H H16A N N N 0 -1.827 -5.524 0.713
52 H16B H H16B N N N 0 -0.699 -4.333 1.404
53 H14 H H14 N N N 0 -3.828 -3.048 -1.216
54 H14A H H14A N N N 0 -3.654 -4.774 -0.816
55 H14B H H14B N N N 0 -4.219 -3.626 0.421
56 HN23 H HN23 N N N 0 4.3 0.428 0.49
57 HN19 H HN19 N N N 0 0.179 0.068 -1.033
58 H20 H H20 N N N 0 1.797 1.335 0.904
59 H20A H H20A N N N 0 1.842 -0.42 1.197
60 H24 H H24 N N N 0 4.836 -0.869 -1.961
61 HN3A H HN3A N N N 0 11.806 1.917 1.0
62 H24A H H24A N N N 0 4.791 0.886 -2.254
63 H30 H H30 N N N 0 6.546 -1.851 -0.552
64 H29 H H29 N N N 0 8.827 -1.653 0.347
65 HN32 H HN32 N N N 0 11.83 -0.375 1.368
66 HN33 H HN33 N N N 0 10.435 2.622 0.333
67 H27 H H27 N N N 0 8.718 2.574 -0.359
68 H26 H H26 N N N 0 6.441 2.354 -1.262



TFN : Chemical Bonds

Total Number of Bonds: 69
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C5 C4 C C doub 1.38 N Y
2 C3 C4 C C sing 1.38 N Y
3 C4 H4 C H sing 1.08 N N
4 C2 C3 C C doub 1.38 N Y
5 C3 H3 C H sing 1.08 N N
6 C1 C2 C C sing 1.38 N Y
7 C2 H2 C H sing 1.08 N N
8 C1 C6 C C doub 1.38 N Y
9 C1 H1 C H sing 1.08 N N
10 C6 C5 C C sing 1.38 N Y
11 C6 H6 C H sing 1.08 N N
12 C5 C7 C C sing 1.51 N N
13 C7 S8 C S sing 1.81 N N
14 C7 H7 C H sing 1.09 N N
15 C7 H7A C H sing 1.09 N N
16 O35 S8 O S doub 1.42 N N
17 S8 N9 S N sing 1.66 N N
18 S8 O34 S O doub 1.42 N N
19 C10 N9 C N sing 1.46 N N
20 N9 HN9 N H sing 0.97 N N
21 C17 C10 C C sing 1.51 N N
22 C10 C11 C C sing 1.53 N N
23 C10 H10 C H sing 1.09 N N
24 O12 C11 O C sing 1.43 N N
25 C11 H11 C H sing 1.09 N N
26 C11 H11A C H sing 1.09 N N
27 O12 C13 O C sing 1.43 N N
28 C16 C13 C C sing 1.53 N N
29 C14 C13 C C sing 1.53 N N
30 C13 C15 C C sing 1.53 N N
31 C15 H15 C H sing 1.09 N N
32 C15 H15A C H sing 1.09 N N
33 C15 H15B C H sing 1.09 N N
34 C16 H16 C H sing 1.09 N N
35 C16 H16A C H sing 1.09 N N
36 C16 H16B C H sing 1.09 N N
37 C14 H14 C H sing 1.09 N N
38 C14 H14A C H sing 1.09 N N
39 C14 H14B C H sing 1.09 N N
40 N19 C17 N C sing 1.35 N N
41 C17 O18 C O doub 1.21 N N
42 C20 N19 C N sing 1.47 N N
43 N19 HN19 N H sing 0.97 N N
44 C21 C20 C C sing 1.51 N N
45 C20 H20 C H sing 1.09 N N
46 C20 H20A C H sing 1.09 N N
47 N23 C21 N C sing 1.35 N N
48 C21 O22 C O doub 1.21 N N
49 C24 N23 C N sing 1.46 N N
50 N23 HN23 N H sing 0.97 N N
51 C24 C25 C C sing 1.51 N N
52 C24 H24 C H sing 1.09 N N
53 C24 H24A C H sing 1.09 N N
54 C26 C25 C C doub 1.38 N Y
55 C25 C30 C C sing 1.38 N Y
56 C30 C29 C C doub 1.38 N Y
57 C30 H30 C H sing 1.08 N N
58 C28 C29 C C sing 1.39 N Y
59 C29 H29 C H sing 1.08 N N
60 C26 C27 C C sing 1.38 N Y
61 C26 H26 C H sing 1.08 N N
62 C27 C28 C C doub 1.39 N Y
63 C27 H27 C H sing 1.08 N N
64 C28 C31 C C sing 1.48 N N
65 N32 C31 N C doub 1.3 N N
66 C31 N33 C N sing 1.38 N N
67 N33 HN33 N H sing 0.97 N N
68 N33 HN3A N H sing 0.97 N N
69 N32 HN32 N H sing 0.97 N N



TFN : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
TFN 3pm3 Open in New Window Bound ligand 1 1