Chemical Components in the PDB

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6U3 : Summary

Code

6U3

One-letter code

X

Molecule name

2-[1-[(2~{R})-2-(2-methoxyphenyl)-2-(oxan-4-yloxy)ethyl]-5-methyl-6-(1,3-oxazol-2-yl)-2,4-bis(oxidanylidene)thieno[2,3-d]pyrimidin-3-yl]-2-methyl-propanamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.5 2-[1-[(2~{R})-2-(2-methoxyphenyl)-2-(oxan-4-yloxy)ethyl]-5-methyl-6-(1,3-oxazol-2-yl)-2,4-bis(oxidanylidene)thieno[2,3-d]pyrimidin-3-yl]-2-methyl-propanamide

Formula

C28 H32 N4 O7 S

Formal charge

0

Molecular weight

568.641 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 COc1ccccc1[CH](CN2C(=O)N(C(=O)c3c(C)c(sc23)c4occn4)C(C)(C)C(N)=O)OC5CCOCC5
SMILES OpenEye OEToolkits 2.0.5 Cc1c2c(sc1c3ncco3)N(C(=O)N(C2=O)C(C)(C)C(=O)N)CC(c4ccccc4OC)OC5CCOCC5
Canonical SMILES CACTVS 3.385 COc1ccccc1[C@H](CN2C(=O)N(C(=O)c3c(C)c(sc23)c4occn4)C(C)(C)C(N)=O)OC5CCOCC5
Canonical SMILES OpenEye OEToolkits 2.0.5 Cc1c2c(sc1c3ncco3)N(C(=O)N(C2=O)C(C)(C)C(=O)N)C[C@@H](c4ccccc4OC)OC5CCOCC5

IUPAC InChI

InChI=1S/C28H32N4O7S/c1-16-21-24(33)32(28(2,3)26(29)34)27(35)31(25(21)40-22(16)23-30-11-14-38-23)15-20(39-17-9-12-37-13-10-17)18-7-5-6-8-19(18)36-4/h5-8,11,14,17,20H,9-10,12-13,15H2,1-4H3,(H2,29,34)/t20-/m0/s1

IUPAC InChI key

HSRWXLIYNCKHRZ-FQEVSTJZSA-N
6U3

wwPDB Information

Atom count

72 (40 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-06-23

Last modified at

2016-07-08

Status

Released

Obsoleted

Not Assigned



6U3 : Atoms of Molecule

Total Number of Atoms: 72
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OAX O O1 N Y N 0 3.966 3.502 1.49
2 CAL C C1 N Y N 0 5.131 4.181 1.447
3 CAK C C2 N Y N 0 6.033 3.392 0.836
4 NAT N N1 N Y N 0 5.421 2.243 0.51
5 CBC C C3 N Y N 0 4.168 2.307 0.906
6 CBE C C4 N Y N 0 3.159 1.252 0.738
7 CBA C C5 N Y N 0 3.379 0.067 0.153
8 CAB C C6 N N N 0 4.719 -0.33 -0.414
9 SAY S S1 N Y N 0 1.495 1.359 1.282
10 CBH C C7 N Y N 0 1.135 -0.205 0.695
11 CBI C C8 N Y N 0 2.257 -0.774 0.112
12 CBF C C9 N N N 0 2.122 -2.136 -0.447
13 OAG O O2 N N N 0 3.075 -2.687 -0.967
14 NBM N N2 N N N 0 0.932 -2.758 -0.37
15 CBN C C10 N N N 0 0.786 -4.108 -0.92
16 CAD C C11 N N N 0 -0.248 -4.09 -2.048
17 CAC C C12 N N N 0 2.132 -4.583 -1.47
18 CAZ C C13 N N N 0 0.328 -5.046 0.167
19 OAF O O3 N N N 0 -0.444 -5.945 -0.094
20 NAE N N3 N N N 0 0.776 -4.887 1.428
21 CBG C C14 N N N 0 -0.125 -2.159 0.203
22 OAH O O4 N N N 0 -1.184 -2.754 0.252
23 NBL N N4 N N N 0 -0.047 -0.927 0.727
24 CAS C C15 N N N 0 -1.235 -0.333 1.345
25 CBK C C16 R N N 0 -2.028 0.438 0.288
26 OAW O O5 N N N 0 -1.21 1.472 -0.261
27 CBJ C C17 N N N 0 -1.515 1.796 -1.619
28 CAQ C C18 N N N 0 -0.247 2.282 -2.328
29 CAO C C19 N N N 0 -0.6 2.7 -3.758
30 OAV O O6 N N N 0 -1.604 3.716 -3.721
31 CAP C C20 N N N 0 -2.829 3.304 -3.112
32 CAR C C21 N N N 0 -2.566 2.91 -1.656
33 CBD C C22 N Y N 0 -3.251 1.048 0.924
34 CAN C C23 N Y N 0 -3.216 2.354 1.374
35 CAJ C C24 N Y N 0 -4.337 2.915 1.958
36 CAI C C25 N Y N 0 -5.495 2.171 2.092
37 CAM C C26 N Y N 0 -5.535 0.865 1.643
38 CBB C C27 N Y N 0 -4.413 0.302 1.052
39 OAU O O7 N N N 0 -4.45 -0.983 0.609
40 CAA C C28 N N N 0 -5.676 -1.695 0.786
41 H1 H H1 N N N 0 5.307 5.175 1.832
42 H2 H H2 N N N 0 7.066 3.64 0.642
43 H3 H H3 N N N 0 5.307 -0.824 0.359
44 H4 H H4 N N N 0 4.572 -1.012 -1.251
45 H5 H H5 N N N 0 5.245 0.56 -0.758
46 H6 H H6 N N N 0 0.083 -3.412 -2.834
47 H7 H H7 N N N 0 -0.357 -5.095 -2.457
48 H8 H H8 N N N 0 -1.208 -3.752 -1.656
49 H9 H H9 N N N 0 2.869 -4.595 -0.667
50 H10 H H10 N N N 0 2.023 -5.587 -1.879
51 H11 H H11 N N N 0 2.463 -3.904 -2.256
52 H12 H H12 N N N 0 1.335 -4.126 1.651
53 H13 H H13 N N N 0 0.539 -5.532 2.112
54 H14 H H14 N N N 0 -1.86 -1.123 1.764
55 H15 H H15 N N N 0 -0.93 0.348 2.139
56 H16 H H16 N N N 0 -2.334 -0.244 -0.506
57 H17 H H17 N N N 0 -1.901 0.912 -2.127
58 H18 H H18 N N N 0 0.167 3.134 -1.79
59 H19 H H19 N N N 0 0.486 1.476 -2.355
60 H20 H H20 N N N 0 0.291 3.087 -4.253
61 H21 H H21 N N N 0 -0.975 1.837 -4.307
62 H22 H H22 N N N 0 -3.544 4.126 -3.142
63 H23 H H23 N N N 0 -3.234 2.449 -3.653
64 H24 H H24 N N N 0 -3.491 2.553 -1.203
65 H25 H H25 N N N 0 -2.199 3.775 -1.105
66 H26 H H26 N N N 0 -2.313 2.936 1.271
67 H27 H H27 N N N 0 -4.308 3.935 2.31
68 H28 H H28 N N N 0 -6.369 2.612 2.548
69 H29 H H29 N N N 0 -6.439 0.285 1.748
70 H30 H H30 N N N 0 -5.918 -1.744 1.847
71 H31 H H31 N N N 0 -6.475 -1.179 0.254
72 H32 H H32 N N N 0 -5.569 -2.705 0.391



6U3 : Chemical Bonds

Total Number of Bonds: 76
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAL OAX C O sing 1.35 N Y
2 CAL CAK C C doub 1.35 N Y
3 CAI CAJ C C doub 1.38 N Y
4 CAI CAM C C sing 1.38 N Y
5 CAJ CAN C C sing 1.38 N Y
6 OAX CBC O C sing 1.35 N Y
7 CAM CBB C C doub 1.39 N Y
8 CAK NAT C N sing 1.34 N Y
9 CAN CBD C C doub 1.38 N Y
10 CBC NAT C N doub 1.32 N Y
11 CBC CBE C C sing 1.47 N N
12 CBB CBD C C sing 1.39 N Y
13 CBB OAU C O sing 1.36 N N
14 CBD CBK C C sing 1.51 N N
15 SAY CBE S C sing 1.75 N Y
16 SAY CBH S C sing 1.71 N Y
17 CBE CBA C C doub 1.34 N Y
18 OAU CAA O C sing 1.43 N N
19 CAS CBK C C sing 1.53 N N
20 CAS NBL C N sing 1.46 N N
21 CBK OAW C O sing 1.43 N N
22 OAW CBJ O C sing 1.43 N N
23 CBH NBL C N sing 1.39 N N
24 CBH CBI C C doub 1.39 N Y
25 CBA CBI C C sing 1.4 N Y
26 CBA CAB C C sing 1.51 N N
27 NBL CBG N C sing 1.34 N N
28 CAR CBJ C C sing 1.53 N N
29 CAR CAP C C sing 1.53 N N
30 CBI CBF C C sing 1.48 N N
31 CBJ CAQ C C sing 1.53 N N
32 CBG OAH C O doub 1.22 N N
33 CBG NBM C N sing 1.34 N N
34 CAP OAV C O sing 1.43 N N
35 CBF NBM C N sing 1.34 N N
36 CBF OAG C O doub 1.22 N N
37 CAQ CAO C C sing 1.53 N N
38 NBM CBN N C sing 1.47 N N
39 OAV CAO O C sing 1.43 N N
40 CBN CAD C C sing 1.53 N N
41 CBN CAC C C sing 1.53 N N
42 CBN CAZ C C sing 1.51 N N
43 CAZ OAF C O doub 1.21 N N
44 CAZ NAE C N sing 1.35 N N
45 CAL H1 C H sing 1.08 N N
46 CAK H2 C H sing 1.08 N N
47 CAB H3 C H sing 1.09 N N
48 CAB H4 C H sing 1.09 N N
49 CAB H5 C H sing 1.09 N N
50 CAD H6 C H sing 1.09 N N
51 CAD H7 C H sing 1.09 N N
52 CAD H8 C H sing 1.09 N N
53 CAC H9 C H sing 1.09 N N
54 CAC H10 C H sing 1.09 N N
55 CAC H11 C H sing 1.09 N N
56 NAE H12 N H sing 0.97 N N
57 NAE H13 N H sing 0.97 N N
58 CAS H14 C H sing 1.09 N N
59 CAS H15 C H sing 1.09 N N
60 CBK H16 C H sing 1.09 N N
61 CBJ H17 C H sing 1.09 N N
62 CAQ H18 C H sing 1.09 N N
63 CAQ H19 C H sing 1.09 N N
64 CAO H20 C H sing 1.09 N N
65 CAO H21 C H sing 1.09 N N
66 CAP H22 C H sing 1.09 N N
67 CAP H23 C H sing 1.09 N N
68 CAR H24 C H sing 1.09 N N
69 CAR H25 C H sing 1.09 N N
70 CAN H26 C H sing 1.08 N N
71 CAJ H27 C H sing 1.08 N N
72 CAI H28 C H sing 1.08 N N
73 CAM H29 C H sing 1.08 N N
74 CAA H30 C H sing 1.09 N N
75 CAA H31 C H sing 1.09 N N
76 CAA H32 C H sing 1.09 N N



6U3 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
6U3 5kkn Open in New Window Bound ligand 2 1