Chemical Components in the PDB

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KU2 : Summary

Code

KU2

One-letter code

X

Molecule name

2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-(2-phenoxyethyl)-1,6-dihydropyrimidine-4 -carboxamide

Synonyms

SRI-30023

Systematic names

ProgramVersionName
ACDLabs 12.01 2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-(2-phenoxyethyl)-1,6-dihydropyrimidine-4-carboxamide
OpenEye OEToolkits 2.0.6 2-[(2~{S})-1-[2-(2-chlorophenyl)sulfanylethanoyl]pyrrolidin-2-yl]-5-oxidanyl-6-oxidanylidene-~{N}-(2-phenoxyethyl)-1~{H}-pyrimidine-4-carboxamide

Formula

C25 H25 Cl N4 O5 S

Formal charge

0

Molecular weight

529.008 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C(CSc1c(cccc1)Cl)(N4C(C=3NC(C(=C(C(=O)NCCOc2ccccc2)N=3)O)=O)CCC4)=O
SMILES CACTVS 3.385 OC1=C(N=C(NC1=O)[CH]2CCCN2C(=O)CSc3ccccc3Cl)C(=O)NCCOc4ccccc4
SMILES OpenEye OEToolkits 2.0.6 c1ccc(cc1)OCCNC(=O)C2=C(C(=O)NC(=N2)C3CCCN3C(=O)CSc4ccccc4Cl)O
Canonical SMILES CACTVS 3.385 OC1=C(N=C(NC1=O)[C@@H]2CCCN2C(=O)CSc3ccccc3Cl)C(=O)NCCOc4ccccc4
Canonical SMILES OpenEye OEToolkits 2.0.6 c1ccc(cc1)OCCNC(=O)C2=C(C(=O)NC(=N2)[C@@H]3CCCN3C(=O)CSc4ccccc4Cl)O

IUPAC InChI

InChI=1S/C25H25ClN4O5S/c26-17-9-4-5-11-19(17)36-15-20(31)30-13-6-10-18(30)23-28-21(22(32)25(34)29-23)24(33)27-12-14-35-16-7-2-1-3-8-16/h1-5,7-9,11,18,32H,6,10,12-15H2,(H,27,33)(H,28,29,34)/t18-/m0/s1

IUPAC InChI key

SAJTUABEFGSMCM-SFHVURJKSA-N
KU2

wwPDB Information

Atom count

61 (36 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-06-27

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



KU2 : Atoms of Molecule

Total Number of Atoms: 61
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N N N 0 2.688 1.522 0.097
2 C13 C C2 N N N 0 -4.462 -2.216 0.681
3 C14 C C3 N Y N 0 6.994 -3.355 -1.574
4 C17 C C4 N Y N 0 5.137 -1.807 -0.226
5 C18 C C5 N Y N 0 5.624 -1.394 -1.46
6 C19 C C6 N Y N 0 6.555 -2.166 -2.128
7 C20 C C7 N Y N 0 -9.1 -2.628 -0.972
8 C21 C C8 N Y N 0 -8.4 -2.037 -2.008
9 C22 C C9 N Y N 0 -7.057 -1.75 -1.861
10 C24 C C10 N Y N 0 -7.114 -2.647 0.366
11 C25 C C11 N Y N 0 -8.457 -2.933 0.213
12 C1 C C12 N N N 0 0.181 3.273 0.316
13 C11 C C13 N N N 0 3.608 0.515 -0.544
14 C12 C C14 N N N 0 -2.962 -1.921 0.614
15 C15 C C15 N Y N 0 6.505 -3.775 -0.351
16 C16 C C16 N Y N 0 5.578 -3.005 0.325
17 C2 C C17 N N N 0 -1.276 1.484 0.527
18 C23 C C18 N Y N 0 -6.41 -2.054 -0.672
19 C3 C C19 N N N 0 -2.302 2.331 0.913
20 C4 C C20 N N N 0 -2.011 3.768 0.986
21 C5 C C21 N N N 0 -1.507 0.025 0.433
22 C6 C C22 N N N 0 2.731 4.546 -1.987
23 C7 C C23 N N N 0 1.493 4.853 -1.104
24 C8 C C24 S N N 0 1.567 3.763 -0.014
25 C9 C C25 N N N 0 2.777 2.999 -1.932
26 N1 N N1 N N N 0 -0.065 1.998 0.242
27 N2 N N2 N N N 0 -0.759 4.177 0.684
28 N3 N N3 N N N 0 -2.75 -0.472 0.593
29 N4 N N4 N N N 0 2.372 2.658 -0.556
30 O1 O O1 N N N 0 -3.534 1.849 1.212
31 O2 O O2 N N N 0 -2.869 4.567 1.319
32 O3 O O3 N N N 0 -0.576 -0.725 0.213
33 O4 O O4 N N N 0 2.229 1.309 1.199
34 O5 O O5 N N N 0 -5.089 -1.773 -0.524
35 S1 S S1 N N N 0 3.955 -0.821 0.632
36 CL1 CL CL1 N N N 0 4.973 -3.526 1.867
37 H1 H H1 N N N 0 -4.616 -3.289 0.798
38 H2 H H2 N N N 0 -4.898 -1.691 1.531
39 H3 H H3 N N N 0 7.719 -3.959 -2.101
40 H4 H H4 N N N 0 5.281 -0.466 -1.894
41 H5 H H5 N N N 0 6.94 -1.841 -3.083
42 H6 H H6 N N N 0 -10.151 -2.847 -1.088
43 H7 H H7 N N N 0 -8.904 -1.8 -2.934
44 H8 H H8 N N N 0 -6.511 -1.289 -2.67
45 H9 H H9 N N N 0 -6.613 -2.886 1.293
46 H10 H H10 N N N 0 -9.006 -3.394 1.021
47 H11 H H11 N N N 0 3.131 0.102 -1.433
48 H12 H H12 N N N 0 4.541 1.003 -0.826
49 H13 H H13 N N N 0 -2.468 -2.348 1.487
50 H14 H H14 N N N 0 -2.545 -2.363 -0.291
51 H15 H H15 N N N 0 6.847 -4.706 0.076
52 H16 H H16 N N N 0 2.579 4.897 -3.008
53 H17 H H17 N N N 0 3.634 4.98 -1.559
54 H18 H H18 N N N 0 1.571 5.846 -0.661
55 H19 H H19 N N N 0 0.574 4.761 -1.683
56 H20 H H20 N N N 0 2.041 4.165 0.881
57 H21 H H21 N N N 0 2.076 2.573 -2.65
58 H22 H H22 N N N 0 3.787 2.642 -2.132
59 H23 H H23 N N N 0 -0.532 5.119 0.731
60 H24 H H24 N N N 0 -3.503 0.13 0.693
61 H25 H H25 N N N 0 -4.171 2.529 1.469



KU2 : Chemical Bonds

Total Number of Bonds: 64
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C20 C25 C C doub 1.38 N Y
2 C20 C21 C C sing 1.38 N Y
3 C25 C24 C C sing 1.38 N Y
4 C21 C22 C C doub 1.38 N Y
5 C24 C23 C C doub 1.39 N Y
6 C22 C23 C C sing 1.39 N Y
7 C23 O5 C O sing 1.36 N N
8 O5 C13 O C sing 1.43 N N
9 C13 C12 C C sing 1.53 N N
10 C18 C19 C C doub 1.38 N Y
11 C18 C17 C C sing 1.39 N Y
12 C19 C14 C C sing 1.38 N Y
13 S1 C17 S C sing 1.76 N N
14 S1 C11 S C sing 1.81 N N
15 O4 C10 O C doub 1.21 N N
16 C17 C16 C C doub 1.39 N Y
17 C14 C15 C C doub 1.38 N Y
18 C12 N3 C N sing 1.46 N N
19 C10 C11 C C sing 1.51 N N
20 C10 N4 C N sing 1.35 N N
21 C16 C15 C C sing 1.38 N Y
22 C16 CL1 C CL sing 1.74 N N
23 N3 C5 N C sing 1.35 N N
24 N4 C9 N C sing 1.47 N N
25 N4 C8 N C sing 1.47 N N
26 C9 C6 C C sing 1.55 N N
27 C5 O3 C O doub 1.22 N N
28 C5 C2 C C sing 1.48 N N
29 N1 C2 N C sing 1.35 N N
30 N1 C1 N C doub 1.3 N N
31 C2 C3 C C doub 1.39 N N
32 C8 C1 C C sing 1.51 N N
33 C8 C7 C C sing 1.54 N N
34 C1 N2 C N sing 1.36 N N
35 C6 C7 C C sing 1.55 N N
36 C3 O1 C O sing 1.36 N N
37 C3 C4 C C sing 1.47 N N
38 N2 C4 N C sing 1.35 N N
39 C4 O2 C O doub 1.22 N N
40 C13 H1 C H sing 1.09 N N
41 C13 H2 C H sing 1.09 N N
42 C14 H3 C H sing 1.08 N N
43 C18 H4 C H sing 1.08 N N
44 C19 H5 C H sing 1.08 N N
45 C20 H6 C H sing 1.08 N N
46 C21 H7 C H sing 1.08 N N
47 C22 H8 C H sing 1.08 N N
48 C24 H9 C H sing 1.08 N N
49 C25 H10 C H sing 1.08 N N
50 C11 H11 C H sing 1.09 N N
51 C11 H12 C H sing 1.09 N N
52 C12 H13 C H sing 1.09 N N
53 C12 H14 C H sing 1.09 N N
54 C15 H15 C H sing 1.08 N N
55 C6 H16 C H sing 1.09 N N
56 C6 H17 C H sing 1.09 N N
57 C7 H18 C H sing 1.09 N N
58 C7 H19 C H sing 1.09 N N
59 C8 H20 C H sing 1.09 N N
60 C9 H21 C H sing 1.09 N N
61 C9 H22 C H sing 1.09 N N
62 N2 H23 N H sing 0.97 N N
63 N3 H24 N H sing 0.97 N N
64 O1 H25 O H sing 0.97 N N



KU2 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
KU2 5w9g Open in New Window Bound ligand 1 1
KU2 5wf3 Open in New Window Bound ligand 1 1