Chemical Components in the PDB

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B3J : Summary

Code

B3J

One-letter code

X

Molecule name

(1S,2S)-2-{[N-({[4-benzyl-1-(tert-butoxycarbonyl)piperidin-4-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (1S,2S)-2-{[N-({[4-benzyl-1-(tert-butoxycarbonyl)piperidin-4-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
OpenEye OEToolkits 2.0.6 (1~{S},2~{S})-2-[[(2~{S})-4-methyl-2-[[1-[(2-methylpropan-2-yl)oxycarbonyl]-4-(phenylmethyl)piperidin-4-yl]oxycarbonylamino]pentanoyl]amino]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propane-1-sulfonic acid

Formula

C31 H48 N4 O10 S

Formal charge

0

Molecular weight

668.799 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C(CC1CCNC1=O)(C(O)S(=O)(O)=O)NC(C(CC(C)C)NC(=O)OC3(Cc2ccccc2)CCN(CC3)C(OC(C)(C)C)=O)=O
SMILES CACTVS 3.385 CC(C)C[CH](NC(=O)OC1(CCN(CC1)C(=O)OC(C)(C)C)Cc2ccccc2)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)[S](O)(=O)=O
SMILES OpenEye OEToolkits 2.0.6 CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OC2(CCN(CC2)C(=O)OC(C)(C)C)Cc3ccccc3
Canonical SMILES CACTVS 3.385 CC(C)C[C@H](NC(=O)OC1(CCN(CC1)C(=O)OC(C)(C)C)Cc2ccccc2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@@H](O)[S](O)(=O)=O
Canonical SMILES OpenEye OEToolkits 2.0.6 CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@@H](O)S(=O)(=O)O)NC(=O)OC2(CCN(CC2)C(=O)OC(C)(C)C)Cc3ccccc3

IUPAC InChI

InChI=1S/C31H48N4O10S/c1-20(2)17-23(26(37)33-24(27(38)46(41,42)43)18-22-11-14-32-25(22)36)34-28(39)44-31(19-21-9-7-6-8-10-21)12-15-35(16-13-31)29(40)45-30(3,4)5/h6-10,20,22-24,27,38H,11-19H2,1-5H3,(H,32,36)(H,33,37)(H,34,39)(H,41,42,43)/t22-,23-,24-,27-/m0/s1

IUPAC InChI key

PJEUBFINPIVQHS-TTZMFTMZSA-N
B3J

wwPDB Information

Atom count

94 (46 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-07-31

Last modified at

2020-05-27

Status

Released

Obsoleted

Not Assigned



B3J : Atoms of Molecule

Total Number of Atoms: 94
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 -4.432 -0.082 -0.332
2 C12 C C2 N N N 0 -5.431 -0.599 0.705
3 C13 C C3 S N N 0 -4.721 -1.555 1.666
4 C14 C C4 N N N 0 -5.688 -2.076 2.706
5 C24 C C5 N N N 0 4.021 2.105 1.383
6 C25 C C6 N Y N 0 4.3 3.321 0.539
7 C16 C C7 N N N 0 -4.475 -3.919 1.982
8 C02 C C8 N N N 0 1.408 1.156 0.412
9 C04 C C9 S N N 0 -1.013 1.413 0.522
10 C05 C C10 N N N 0 -1.386 2.894 0.613
11 C06 C C11 N N N 0 -0.339 3.632 1.45
12 C07 C C12 N N N 0 -0.627 5.135 1.416
13 C08 C C13 N N N 0 -0.399 3.135 2.896
14 C09 C C14 N N N 0 -2.116 0.659 -0.175
15 C17 C C15 N N N 0 -4.249 -2.823 0.917
16 C19 C C16 S N N 0 -5.149 0.851 -1.31
17 C26 C C18 N Y N 0 5.6 3.643 0.197
18 C27 C C19 N Y N 0 5.856 4.759 -0.577
19 C28 C C20 N Y N 0 4.811 5.553 -1.011
20 C29 C C21 N Y N 0 3.51 5.231 -0.671
21 C30 C C22 N Y N 0 3.254 4.113 0.1
22 N03 N N1 N N N 0 0.232 1.269 -0.237
23 N10 N N2 N N N 0 -3.359 0.65 0.345
24 N15 N N3 N N N 0 -5.532 -3.402 2.858
25 O01 O O1 N N N 0 1.429 1.106 1.626
26 O18 O O2 N N N 0 -6.487 -1.396 3.314
27 O20 O O3 N N N 0 -4.192 1.442 -2.192
28 O21 O O4 N N N 0 -1.885 0.06 -1.204
29 O22 O O5 N N N 0 2.559 1.1 -0.285
30 S S S1 N N N 0 -6.357 -0.097 -2.276
31 H1 H H1 N N N 0 -4.008 -0.925 -0.879
32 H2 H H2 N N N 0 -5.84 0.242 1.266
33 H3 H H3 N N N 0 -6.24 -1.126 0.199
34 H4 H H4 N N N 0 -3.876 -1.057 2.142
35 H5 H H5 N N N 0 4.876 1.908 2.029
36 H6 H H6 N N N 0 3.136 2.282 1.995
37 H7 H H7 N N N 0 -4.798 -4.846 1.507
38 H8 H H8 N N N 0 -3.561 -4.087 2.552
39 H9 H H9 N N N 0 -0.875 1.01 1.525
40 H10 H H10 N N N 0 -1.419 3.323 -0.388
41 H11 H H11 N N N 0 -2.364 2.994 1.084
42 H12 H H12 N N N 0 0.653 3.443 1.041
43 H13 H H13 N N N 0 0.119 5.661 2.012
44 H14 H H14 N N N 0 -0.584 5.489 0.386
45 H15 H H15 N N N 0 -1.619 5.324 1.825
46 H16 H H16 N N N 0 -1.36 3.405 3.334
47 H17 H H17 N N N 0 -0.284 2.051 2.912
48 H18 H H18 N N N 0 0.405 3.594 3.471
49 H19 H H19 N N N 0 -4.862 -3.005 0.034
50 H20 H H20 N N N 0 -3.195 -2.749 0.65
51 H21 H H21 N N N 0 -5.663 1.635 -0.753
52 H24 H H24 N N N 0 6.416 3.023 0.536
53 H25 H H25 N N N 0 6.872 5.011 -0.843
54 H26 H H26 N N N 0 5.01 6.425 -1.616
55 H27 H H27 N N N 0 2.694 5.852 -1.01
56 H28 H H28 N N N 0 2.238 3.859 0.363
57 H29 H H29 N N N 0 0.21 1.254 -1.207
58 H30 H H30 N N N 0 -3.544 1.129 1.168
59 H31 H H31 N N N 0 -6.052 -3.948 3.469
60 H32 H H32 N N N 0 -3.514 1.965 -1.743
61 O2 O O6 N N N 0 -5.786 -1.317 -2.728
62 O3 O O7 N N N 0 -7.403 -0.527 -1.258
63 O1 O O8 N N N 0 -7.063 0.756 -3.166
64 C1 C C23 N N N 0 4.959 0.741 -0.488
65 C2 C C24 N N N 0 4.698 -0.448 -1.419
66 N1 N N4 N N N 0 4.424 -1.637 -0.602
67 C4 C C25 N N N 0 3.369 -1.566 0.419
68 C5 C C26 N N N 0 3.645 -0.365 1.329
69 C23 C C27 N N N 0 3.78 0.898 0.474
70 H33 H H33 N N Y 0 -8.125 -1.05 -1.633
71 H34 H H34 N N N 0 5.872 0.564 0.08
72 H35 H H35 N N N 0 5.069 1.649 -1.081
73 H36 H H36 N N N 0 3.837 -0.233 -2.053
74 H37 H H37 N N N 0 5.576 -0.625 -2.04
75 H40 H H40 N N N 0 2.4 -1.443 -0.065
76 H41 H H41 N N N 0 3.371 -2.481 1.011
77 H42 H H42 N N N 0 2.82 -0.243 2.03
78 H43 H H43 N N N 0 4.57 -0.531 1.88
79 C3 C C28 N N N 0 5.126 -2.773 -0.785
80 O5 O O9 N N N 0 4.864 -3.856 -0.029
81 C15 C C32 N N N 0 5.457 -5.495 -1.729
82 C8 C C29 N N N 0 5.659 -5.044 -0.282
83 C9 C C30 N N N 0 7.138 -4.727 -0.048
84 C10 C C31 N N N 0 5.221 -6.162 0.667
85 O4 O O10 N N N 0 5.995 -2.82 -1.633
86 H22 H H22 N N N 0 7.282 -4.406 0.984
87 H23 H H23 N N N 0 7.735 -5.619 -0.237
88 H38 H H38 N N N 0 7.45 -3.931 -0.724
89 H39 H H39 N N N 0 4.168 -6.388 0.501
90 H44 H H44 N N N 0 5.818 -7.054 0.477
91 H45 H H45 N N N 0 5.365 -5.841 1.698
92 H46 H H46 N N N 0 5.769 -4.699 -2.405
93 H47 H H47 N N N 0 6.054 -6.387 -1.919
94 H48 H H48 N N N 0 4.404 -5.721 -1.896



B3J : 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 C07 C06 C C sing 1.53 N N
2 C06 C08 C C sing 1.53 N N
3 C06 C05 C C sing 1.53 N N
4 C05 C04 C C sing 1.53 N N
5 N03 C04 N C sing 1.47 N N
6 N03 C02 N C sing 1.35 N N
7 C04 C09 C C sing 1.51 N N
8 O22 C02 O C sing 1.35 N N
9 O22 C23 O C sing 1.45 N N
10 C02 O01 C O doub 1.22 N N
11 C23 C24 C C sing 1.53 N N
12 C09 O21 C O doub 1.21 N N
13 C09 N10 C N sing 1.35 N N
14 C24 C25 C C sing 1.51 N N
15 N10 C11 N C sing 1.46 N N
16 C26 C25 C C doub 1.38 N Y
17 C26 C27 C C sing 1.38 N Y
18 C25 C30 C C sing 1.38 N Y
19 S C19 S C sing 1.81 N N
20 C19 C11 C C sing 1.53 N N
21 C19 O20 C O sing 1.43 N N
22 C11 C12 C C sing 1.53 N N
23 C27 C28 C C doub 1.38 N Y
24 C30 C29 C C doub 1.38 N Y
25 C28 C29 C C sing 1.38 N Y
26 C12 C13 C C sing 1.53 N N
27 C13 C17 C C sing 1.55 N N
28 C13 C14 C C sing 1.51 N N
29 C17 C16 C C sing 1.54 N N
30 C14 O18 C O doub 1.21 N N
31 C14 N15 C N sing 1.34 N N
32 C16 N15 C N sing 1.47 N N
33 C11 H1 C H sing 1.09 N N
34 C12 H2 C H sing 1.09 N N
35 C12 H3 C H sing 1.09 N N
36 C13 H4 C H sing 1.09 N N
37 C24 H5 C H sing 1.09 N N
38 C24 H6 C H sing 1.09 N N
39 C16 H7 C H sing 1.09 N N
40 C16 H8 C H sing 1.09 N N
41 C04 H9 C H sing 1.09 N N
42 C05 H10 C H sing 1.09 N N
43 C05 H11 C H sing 1.09 N N
44 C06 H12 C H sing 1.09 N N
45 C07 H13 C H sing 1.09 N N
46 C07 H14 C H sing 1.09 N N
47 C07 H15 C H sing 1.09 N N
48 C08 H16 C H sing 1.09 N N
49 C08 H17 C H sing 1.09 N N
50 C08 H18 C H sing 1.09 N N
51 C17 H19 C H sing 1.09 N N
52 C17 H20 C H sing 1.09 N N
53 C19 H21 C H sing 1.09 N N
54 C26 H24 C H sing 1.08 N N
55 C27 H25 C H sing 1.08 N N
56 C28 H26 C H sing 1.08 N N
57 C29 H27 C H sing 1.08 N N
58 C30 H28 C H sing 1.08 N N
59 N03 H29 N H sing 0.97 N N
60 N10 H30 N H sing 0.97 N N
61 N15 H31 N H sing 0.97 N N
62 O20 H32 O H sing 0.97 N N
63 S O2 S O doub 1.42 N N
64 S O3 S O sing 1.52 N N
65 S O1 S O doub 1.42 N N
66 C23 C1 C C sing 1.53 N N
67 C1 C2 C C sing 1.53 N N
68 C2 N1 C N sing 1.47 N N
69 N1 C4 N C sing 1.47 N N
70 C4 C5 C C sing 1.53 N N
71 C5 C23 C C sing 1.53 N N
72 O3 H33 O H sing 0.97 N N
73 C1 H34 C H sing 1.09 N N
74 C1 H35 C H sing 1.09 N N
75 C2 H36 C H sing 1.09 N N
76 C2 H37 C H sing 1.09 N N
77 C4 H40 C H sing 1.09 N N
78 C4 H41 C H sing 1.09 N N
79 C5 H42 C H sing 1.09 N N
80 C5 H43 C H sing 1.09 N N
81 N1 C3 N C sing 1.35 N N
82 C3 O5 C O sing 1.35 N N
83 O5 C8 O C sing 1.45 N N
84 C8 C9 C C sing 1.53 N N
85 C8 C10 C C sing 1.53 N N
86 C8 C15 C C sing 1.53 N N
87 C3 O4 C O doub 1.22 N N
88 C9 H22 C H sing 1.09 N N
89 C9 H23 C H sing 1.09 N N
90 C9 H38 C H sing 1.09 N N
91 C10 H39 C H sing 1.09 N N
92 C10 H44 C H sing 1.09 N N
93 C10 H45 C H sing 1.09 N N
94 C15 H46 C H sing 1.09 N N
95 C15 H47 C H sing 1.09 N N
96 C15 H48 C H sing 1.09 N N



B3J : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
B3J 5wkl Open in New Window Bound ligand 1 1