Chemical Components in the PDB

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BXD : Summary

Code

BXD

One-letter code

X

Molecule name

(3S,4S,5R)-3-(4-amino-3-{[(2R)-3-ethoxy-1,1,1-trifluoropropan-2-yl]oxy}-5-fluorobenzyl)-5-[(3-tert-butylbenzyl)amino]tetrahydro-2H-thiopyran-4-ol 1,1-dioxide

Systematic names

ProgramVersionName
ACDLabs 12.01 (3S,4S,5R)-3-(4-amino-3-{[(2R)-3-ethoxy-1,1,1-trifluoropropan-2-yl]oxy}-5-fluorobenzyl)-5-[(3-tert-butylbenzyl)amino]tetrahydro-2H-thiopyran-4-ol 1,1-dioxide
OpenEye OEToolkits 1.7.6 (3S,4S,5R)-3-[[4-azanyl-3-[(2R)-3-ethoxy-1,1,1-tris(fluoranyl)propan-2-yl]oxy-5-fluoranyl-phenyl]methyl]-5-[(3-tert-butylphenyl)methylamino]-1,1-bis(oxidanylidene)thian-4-ol

Formula

C28 H38 F4 N2 O5 S

Formal charge

0

Molecular weight

590.67 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=S2(=O)CC(C(O)C(NCc1cccc(c1)C(C)(C)C)C2)Cc3cc(F)c(N)c(OC(C(F)(F)F)COCC)c3
SMILES CACTVS 3.370 CCOC[CH](Oc1cc(C[CH]2C[S](=O)(=O)C[CH](NCc3cccc(c3)C(C)(C)C)[CH]2O)cc(F)c1N)C(F)(F)F
SMILES OpenEye OEToolkits 1.7.6 CCOCC(C(F)(F)F)Oc1cc(cc(c1N)F)CC2CS(=O)(=O)CC(C2O)NCc3cccc(c3)C(C)(C)C
Canonical SMILES CACTVS 3.370 CCOC[C@@H](Oc1cc(C[C@@H]2C[S](=O)(=O)C[C@H](NCc3cccc(c3)C(C)(C)C)[C@H]2O)cc(F)c1N)C(F)(F)F
Canonical SMILES OpenEye OEToolkits 1.7.6 CCOC[C@H](C(F)(F)F)Oc1cc(cc(c1N)F)C[C@@H]2CS(=O)(=O)C[C@@H]([C@H]2O)NCc3cccc(c3)C(C)(C)C

IUPAC InChI

InChI=1S/C28H38F4N2O5S/c1-5-38-14-24(28(30,31)32)39-23-12-18(11-21(29)25(23)33)9-19-15-40(36,37)16-22(26(19)35)34-13-17-7-6-8-20(10-17)27(2,3)4/h6-8,10-12,19,22,24,26,34-35H,5,9,13-16,33H2,1-4H3/t19-,22+,24-,26+/m1/s1

IUPAC InChI key

UJZFSYZNJMWXJO-NJONLQHESA-N
BXD

wwPDB Information

Atom count

78 (40 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-01-13

Last modified at

2012-11-16

Status

Released

Obsoleted

Not Assigned



BXD : Atoms of Molecule

Total Number of Atoms: 78
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 F1 F F1 N N N 0 -5.056 -1.957 1.74
2 C2 C C2 N N N 0 -4.081 -1.967 0.737
3 F3 F F3 N N N 0 -3.09 -1.027 1.041
4 F4 F F4 N N N 0 -3.507 -3.24 0.658
5 C5 C C5 R N N 0 -4.725 -1.614 -0.605
6 O7 O O7 N N N 0 -5.312 -0.313 -0.524
7 C8 C C8 N Y N 0 -4.497 0.748 -0.77
8 C9 C C9 N Y N 0 -4.972 2.046 -0.602
9 C10 C C10 N Y N 0 -4.136 3.125 -0.855
10 C11 C C11 N Y N 0 -2.834 2.908 -1.273
11 C13 C C13 N Y N 0 -2.365 1.618 -1.438
12 C14 C C14 N Y N 0 -3.191 0.539 -1.183
13 C16 C C16 N N N 0 -0.947 1.387 -1.894
14 C19 C C19 S N N 0 -0.029 1.292 -0.673
15 C21 C C21 S N N 0 1.382 0.93 -1.128
16 C23 C C23 R N N 0 2.261 0.583 0.07
17 C25 C C25 N N N 0 2.55 1.843 0.889
18 S28 S S28 N N N 0 0.988 2.48 1.564
19 C29 C C29 N N N 0 -0.012 2.638 0.056
20 O32 O O32 N N N 0 1.219 3.777 2.097
21 O33 O O33 N N N 0 0.41 1.481 2.393
22 N34 N N34 N N N 0 3.529 0.011 -0.405
23 C36 C C36 N N N 0 4.131 -0.854 0.618
24 C39 C C39 N Y N 0 5.427 -1.42 0.097
25 C40 C C40 N Y N 0 6.612 -0.74 0.304
26 C42 C C42 N Y N 0 7.8 -1.26 -0.174
27 C43 C C43 N Y N 0 7.803 -2.46 -0.86
28 C45 C C45 N Y N 0 6.618 -3.141 -1.067
29 C47 C C47 N Y N 0 5.43 -2.623 -0.584
30 C49 C C49 N N N 0 9.092 -0.518 0.052
31 C50 C C50 N N N 0 9.007 0.865 -0.597
32 C54 C C54 N N N 0 9.335 -0.363 1.554
33 C58 C C58 N N N 0 10.247 -1.304 -0.573
34 O62 O O62 N N N 0 1.32 -0.194 -2.008
35 F64 F F64 N N N 0 -4.592 4.387 -0.695
36 N65 N N65 N N N 0 -6.291 2.263 -0.18
37 C68 C C68 N N N 0 -5.809 -2.642 -0.937
38 O71 O O71 N N N 0 -6.743 -2.715 0.142
39 C72 C C72 N N N 0 -7.802 -3.651 -0.068
40 C75 C C75 N N N 0 -8.736 -3.645 1.144
41 H1 H H1 N N N 0 -3.965 -1.622 -1.386
42 H2 H H2 N N N 0 -2.184 3.747 -1.47
43 H3 H H3 N N N 0 -2.819 -0.467 -1.309
44 H4 H H4 N N N 0 -0.894 0.458 -2.461
45 H5 H H5 N N N 0 -0.628 2.217 -2.524
46 H6 H H6 N N N 0 -0.401 0.52 0.0
47 H7 H H7 N N N 0 1.817 1.777 -1.659
48 H8 H H8 N N N 0 1.747 -0.146 0.696
49 H9 H H9 N N N 0 3.228 1.598 1.707
50 H10 H H10 N N N 0 3.006 2.598 0.25
51 H11 H H11 N N N 0 0.422 3.4 -0.591
52 H12 H H12 N N N 0 -1.031 2.919 0.321
53 H13 H H13 N N N 0 4.169 0.738 -0.688
54 H15 H H15 N N N 0 4.326 -0.27 1.518
55 H16 H H16 N N N 0 3.447 -1.668 0.854
56 H17 H H17 N N N 0 6.61 0.198 0.84
57 H18 H H18 N N N 0 8.731 -2.866 -1.234
58 H19 H H19 N N N 0 6.62 -4.078 -1.604
59 H20 H H20 N N N 0 4.505 -3.157 -0.742
60 H21 H H21 N N N 0 8.184 1.424 -0.152
61 H22 H H22 N N N 0 9.941 1.401 -0.434
62 H23 H H23 N N N 0 8.833 0.754 -1.668
63 H24 H H24 N N N 0 9.397 -1.348 2.016
64 H25 H H25 N N N 0 10.27 0.174 1.717
65 H26 H H26 N N N 0 8.513 0.197 1.999
66 H27 H H27 N N N 0 10.074 -1.414 -1.644
67 H28 H H28 N N N 0 11.182 -0.767 -0.41
68 H29 H H29 N N N 0 10.309 -2.289 -0.111
69 H30 H H30 N N N 0 2.181 -0.483 -2.339
70 H31 H H31 N N N 0 -6.874 1.508 -0.0040
71 H32 H H32 N N N 0 -6.62 3.168 -0.064
72 H33 H H33 N N N 0 -6.328 -2.341 -1.847
73 H34 H H34 N N N 0 -5.349 -3.619 -1.086
74 H35 H H35 N N N 0 -8.362 -3.372 -0.96
75 H36 H H36 N N N 0 -7.383 -4.649 -0.199
76 H37 H H37 N N N 0 -8.175 -3.924 2.036
77 H38 H H38 N N N 0 -9.154 -2.647 1.275
78 H39 H H39 N N N 0 -9.543 -4.359 0.984



BXD : Chemical Bonds

Total Number of Bonds: 80
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O32 S28 O S doub 1.4211471 N N
2 C25 S28 C S sing 1.8169309 N N
3 C25 C23 C C sing 1.5303209 N N
4 S28 O33 S O doub 1.4210299 N N
5 S28 C29 S C sing 1.8163227 N N
6 O71 C68 O C sing 1.4289597 N N
7 O71 C72 O C sing 1.4288726 N N
8 C75 C72 C C sing 1.5301424 N N
9 C36 N34 C N sing 1.4687266 N N
10 C36 C39 C C sing 1.5071207 N N
11 C47 C39 C C doub 1.3823817 N Y
12 C47 C45 C C sing 1.3830969 N Y
13 C68 C5 C C sing 1.5303804 N N
14 N34 C23 N C sing 1.4699092 N N
15 F4 C2 F C sing 1.3986586 N N
16 C29 C19 C C sing 1.5308318 N N
17 C39 C40 C C sing 1.3818371 N Y
18 C23 C21 C C sing 1.5258617 N N
19 C45 C43 C C doub 1.3823296 N Y
20 C5 C2 C C sing 1.5298069 N N
21 C5 O7 C O sing 1.4295912 N N
22 C2 F1 C F sing 1.398833 N N
23 C2 F3 C F sing 1.3993202 N N
24 C21 C19 C C sing 1.5261029 N N
25 C21 O62 C O sing 1.4288527 N N
26 C19 C16 C C sing 1.5305521 N N
27 C40 C42 C C doub 1.38211 N Y
28 C43 C42 C C sing 1.3822464 N Y
29 O7 C8 O C sing 1.3603169 N N
30 C42 C49 C C sing 1.5069519 N N
31 C14 C8 C C doub 1.3855995 N Y
32 C14 C13 C C sing 1.3825853 N Y
33 C16 C13 C C sing 1.5073224 N N
34 C8 C9 C C sing 1.3923552 N Y
35 C13 C11 C C doub 1.3824927 N Y
36 C9 N65 C N sing 1.401761 N N
37 C9 C10 C C doub 1.3882169 N Y
38 C11 C10 C C sing 1.3845638 N Y
39 C50 C49 C C sing 1.5300703 N N
40 C49 C54 C C sing 1.5294044 N N
41 C49 C58 C C sing 1.5305052 N N
42 C10 F64 C F sing 1.3513622 N N
43 C5 H1 C H sing 1.0897821 N N
44 C11 H2 C H sing 1.0794582 N N
45 C14 H3 C H sing 1.0799519 N N
46 C16 H4 C H sing 1.0896509 N N
47 C16 H5 C H sing 1.0897527 N N
48 C19 H6 C H sing 1.0896316 N N
49 C21 H7 C H sing 1.090227 N N
50 C23 H8 C H sing 1.0897307 N N
51 C25 H9 C H sing 1.0903362 N N
52 C25 H10 C H sing 1.0891657 N N
53 C29 H11 C H sing 1.0897747 N N
54 C29 H12 C H sing 1.0897464 N N
55 N34 H13 N H sing 1.0090679 N N
56 C36 H15 C H sing 1.0904499 N N
57 C36 H16 C H sing 1.0891042 N N
58 C40 H17 C H sing 1.0803444 N N
59 C43 H18 C H sing 1.0797666 N N
60 C45 H19 C H sing 1.0799731 N N
61 C47 H20 C H sing 1.0796968 N N
62 C50 H21 C H sing 1.0898784 N N
63 C50 H22 C H sing 1.0891377 N N
64 C50 H23 C H sing 1.0907053 N N
65 C54 H24 C H sing 1.0897307 N N
66 C54 H25 C H sing 1.0904875 N N
67 C54 H26 C H sing 1.089637 N N
68 C58 H27 C H sing 1.0904449 N N
69 C58 H28 C H sing 1.0904875 N N
70 C58 H29 C H sing 1.0897307 N N
71 O62 H30 O H sing 0.96664524 N N
72 N65 H31 N H sing 0.96999484 N N
73 N65 H32 N H sing 0.96990824 N N
74 C68 H33 C H sing 1.0899825 N N
75 C68 H34 C H sing 1.0901055 N N
76 C72 H35 C H sing 1.0895435 N N
77 C72 H36 C H sing 1.0902871 N N
78 C75 H37 C H sing 1.0900578 N N
79 C75 H38 C H sing 1.0899032 N N
80 C75 H39 C H sing 1.0893323 N N



BXD : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
BXD 4d89 Open in New Window Bound ligand 1 1
BXD 4d8c Open in New Window Bound ligand 3 1