Chemical Components in the PDB

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S54 : Summary

Code

S54

One-letter code

X

Molecule name

N-(benzylsulfonyl)-D-valyl-N-(4-carbamimidoylbenzyl)-L-prolinamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-(benzylsulfonyl)-D-valyl-N-(4-carbamimidoylbenzyl)-L-prolinamide
OpenEye OEToolkits 1.7.2 (2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[(2R)-3-methyl-2-[(phenylmethyl)sulfonylamino]butanoyl]pyrrolidine-2-carboxamide

Formula

C25 H33 N5 O4 S

Formal charge

0

Molecular weight

499.626 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NCc1ccc(C(=[N@H])N)cc1)C3N(C(=O)C(NS(=O)(=O)Cc2ccccc2)C(C)C)CCC3
SMILES CACTVS 3.370 CC(C)[CH](N[S](=O)(=O)Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)NCc3ccc(cc3)C(N)=N
SMILES OpenEye OEToolkits 1.7.2 CC(C)C(C(=O)N1CCCC1C(=O)NCc2ccc(cc2)C(=N)N)NS(=O)(=O)Cc3ccccc3
Canonical SMILES CACTVS 3.370 CC(C)[C@@H](N[S](=O)(=O)Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NCc3ccc(cc3)C(N)=N
Canonical SMILES OpenEye OEToolkits 1.7.2 [H]/N=C(/c1ccc(cc1)CNC(=O)[C@@H]2CCCN2C(=O)[C@@H](C(C)C)NS(=O)(=O)Cc3ccccc3)\\N

IUPAC InChI

InChI=1S/C25H33N5O4S/c1-17(2)22(29-35(33,34)16-19-7-4-3-5-8-19)25(32)30-14-6-9-21(30)24(31)28-15-18-10-12-20(13-11-18)23(26)27/h3-5,7-8,10-13,17,21-22,29H,6,9,14-16H2,1-2H3,(H3,26,27)(H,28,31)/t21-,22+/m0/s1

IUPAC InChI key

BTZOUFLORPKMGE-FCHUYYIVSA-N

Has sub-components

PMS , DVA , 00S
S54

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

2011-04-25

Last modified at

2012-04-20

Status

Released

Obsoleted

Not Assigned



S54 : 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 -5.353 0.078 -0.064
2 S8 S S8 N N N 0 -3.964 -0.347 -1.151
3 C4 C C4 N Y N 0 -6.148 -1.164 0.244
4 C5 C C5 N Y N 0 -7.201 -1.531 -0.573
5 C6 C C6 N Y N 0 -7.933 -2.669 -0.289
6 C1 C C1 N Y N 0 -7.609 -3.441 0.811
7 C2 C C2 N Y N 0 -6.556 -3.075 1.628
8 C3 C C3 N Y N 0 -5.826 -1.936 1.344
9 O22 O O22 N N N 0 -3.079 -1.248 -0.499
10 O23 O O23 N N N 0 -4.423 -0.599 -2.472
11 N9 N N9 N N N 0 -3.095 1.056 -1.281
12 C10 C C10 R N N 0 -2.486 1.653 -0.09
13 C18 C C18 N N N 0 -2.898 3.123 0.012
14 C19 C C19 N N N 0 -2.471 3.862 -1.258
15 C20 C C20 N N N 0 -4.417 3.217 0.17
16 C11 C C11 N N N 0 -0.985 1.559 -0.192
17 O17 O O17 N N N 0 -0.459 1.419 -1.276
18 N12 N N12 N N N 0 -0.228 1.63 0.92
19 C13 C C13 S N N 0 1.242 1.655 0.956
20 C24 C C24 N N N 0 1.792 0.407 0.316
21 O33 O O33 N N N 0 1.036 -0.43 -0.13
22 C14 C C14 N N N 0 1.663 1.714 2.44
23 C15 C C15 N N N 0 0.42 1.147 3.176
24 C16 C C16 N N N 0 -0.736 1.701 2.303
25 N25 N N25 N N N 0 3.125 0.22 0.24
26 C26 C C26 N N N 0 3.659 -0.994 -0.382
27 C27 C C27 N Y N 0 5.165 -0.958 -0.341
28 C32 C C32 N Y N 0 5.87 -0.393 -1.389
29 C31 C C31 N Y N 0 7.249 -0.352 -1.354
30 C30 C C30 N Y N 0 7.932 -0.891 -0.264
31 C34 C C34 N N N 0 9.412 -0.855 -0.222
32 N35 N N35 N N N 0 10.048 -1.359 0.797
33 N36 N N36 N N N 0 10.117 -0.289 -1.262
34 C29 C C29 N Y N 0 7.216 -1.464 0.787
35 C28 C C28 N Y N 0 5.838 -1.494 0.743
36 H7 H H7 N N N 0 -5.994 0.806 -0.562
37 H7A H H7A N N N 0 -4.971 0.505 0.863
38 H5 H H5 N N N 0 -7.454 -0.927 -1.432
39 H6 H H6 N N N 0 -8.756 -2.955 -0.927
40 H1 H H1 N N N 0 -8.177 -4.334 1.03
41 H2 H H2 N N N 0 -6.304 -3.678 2.487
42 H3 H H3 N N N 0 -5.003 -1.65 1.982
43 HN9 H HN9 N N N 0 -2.99 1.484 -2.145
44 H10 H H10 N N N 0 -2.824 1.119 0.798
45 H18 H H18 N N N 0 -2.414 3.577 0.877
46 H19 H H19 N N N 0 -3.015 3.46 -2.112
47 H19A H H19A N N N 0 -2.694 4.924 -1.153
48 H19B H H19B N N N 0 -1.401 3.729 -1.413
49 H20 H H20 N N N 0 -4.734 2.595 1.008
50 H20A H H20A N N N 0 -4.7 4.253 0.359
51 H20B H H20B N N N 0 -4.9 2.87 -0.743
52 H13 H H13 N N N 0 1.61 2.537 0.431
53 H14 H H14 N N N 0 2.536 1.086 2.618
54 H14A H H14A N N N 0 1.857 2.742 2.745
55 H15 H H15 N N N 0 0.429 0.057 3.175
56 H15A H H15A N N N 0 0.359 1.534 4.193
57 H16 H H16 N N N 0 -0.958 2.733 2.572
58 H16A H H16A N N N 0 -1.625 1.079 2.412
59 HN25 H HN25 N N N 0 3.729 0.889 0.596
60 H26 H H26 N N N 0 3.302 -1.868 0.161
61 H26A H H26A N N N 0 3.326 -1.048 -1.419
62 H32 H H32 N N N 0 5.34 0.02 -2.234
63 H31 H H31 N N N 0 7.798 0.093 -2.17
64 HN35 H HN35 N N N 0 11.017 -1.335 0.824
65 HN36 H HN36 N N N 0 9.644 0.086 -2.021
66 HN3A H HN3A N N N 0 11.086 -0.265 -1.235
67 H29 H H29 N N N 0 7.74 -1.883 1.634
68 H28 H H28 N N N 0 5.282 -1.938 1.556



S54 : Chemical Bonds

Total Number of Bonds: 70
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C doub 1.38 N Y
2 C1 C6 C C sing 1.38 N Y
3 C2 C3 C C sing 1.38 N Y
4 C3 C4 C C doub 1.38 N Y
5 C4 C5 C C sing 1.38 N Y
6 C4 C7 C C sing 1.51 N N
7 C5 C6 C C doub 1.38 N Y
8 C7 S8 C S sing 1.81 N N
9 S8 N9 S N sing 1.66 N N
10 S8 O22 S O doub 1.42 N N
11 S8 O23 S O doub 1.42 N N
12 N9 C10 N C sing 1.46 N N
13 C10 C11 C C sing 1.51 N N
14 C10 C18 C C sing 1.53 N N
15 C11 N12 C N sing 1.35 N N
16 C11 O17 C O doub 1.21 N N
17 N12 C13 N C sing 1.47 N N
18 N12 C16 N C sing 1.48 N N
19 C13 C14 C C sing 1.54 N N
20 C13 C24 C C sing 1.51 N N
21 C14 C15 C C sing 1.55 N N
22 C15 C16 C C sing 1.55 N N
23 C18 C19 C C sing 1.53 N N
24 C18 C20 C C sing 1.53 N N
25 C24 N25 C N sing 1.35 N N
26 C24 O33 C O doub 1.21 N N
27 N25 C26 N C sing 1.46 N N
28 C26 C27 C C sing 1.51 N N
29 C27 C28 C C doub 1.38 N Y
30 C27 C32 C C sing 1.38 N Y
31 C28 C29 C C sing 1.38 N Y
32 C29 C30 C C doub 1.39 N Y
33 C30 C31 C C sing 1.39 N Y
34 C30 C34 C C sing 1.48 N N
35 C31 C32 C C doub 1.38 N Y
36 C34 N35 C N doub 1.3 N N
37 C34 N36 C N sing 1.38 N N
38 C1 H1 C H sing 1.08 N N
39 C2 H2 C H sing 1.08 N N
40 C3 H3 C H sing 1.08 N N
41 C5 H5 C H sing 1.08 N N
42 C6 H6 C H sing 1.08 N N
43 C7 H7 C H sing 1.09 N N
44 C7 H7A C H sing 1.09 N N
45 N9 HN9 N H sing 0.97 N N
46 C10 H10 C H sing 1.09 N N
47 C13 H13 C H sing 1.09 N N
48 C14 H14 C H sing 1.09 N N
49 C14 H14A C H sing 1.09 N N
50 C15 H15 C H sing 1.09 N N
51 C15 H15A C H sing 1.09 N N
52 C16 H16 C H sing 1.09 N N
53 C16 H16A C H sing 1.09 N N
54 C18 H18 C H sing 1.09 N N
55 C19 H19 C H sing 1.09 N N
56 C19 H19A C H sing 1.09 N N
57 C19 H19B C H sing 1.09 N N
58 C20 H20 C H sing 1.09 N N
59 C20 H20A C H sing 1.09 N N
60 C20 H20B C H sing 1.09 N N
61 N25 HN25 N H sing 0.97 N N
62 C26 H26 C H sing 1.09 N N
63 C26 H26A C H sing 1.09 N N
64 C28 H28 C H sing 1.08 N N
65 C29 H29 C H sing 1.08 N N
66 C31 H31 C H sing 1.08 N N
67 C32 H32 C H sing 1.08 N N
68 N35 HN35 N H sing 0.97 N N
69 N36 HN36 N H sing 0.97 N N
70 N36 HN3A N H sing 0.97 N N



S54 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
S54 3rm0 Open in New Window Bound ligand 2 1