Chemical Components in the PDB

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5CO : Summary

Code

5CO

One-letter code

X

Molecule name

5-chloro-6-ethyl-2-{5-[(4-methylpiperazin-1-yl)sulfonyl]-2-propoxyphenyl}pyrimidin-4(3H)-one

Systematic names

ProgramVersionName
ACDLabs 12.01 5-chloro-6-ethyl-2-{5-[(4-methylpiperazin-1-yl)sulfonyl]-2-propoxyphenyl}pyrimidin-4(3H)-one
OpenEye OEToolkits 1.7.2 5-chloranyl-4-ethyl-2-[5-(4-methylpiperazin-1-yl)sulfonyl-2-propoxy-phenyl]-1H-pyrimidin-6-one

Formula

C20 H27 Cl N4 O4 S

Formal charge

0

Molecular weight

454.971 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=S(=O)(c2cc(C1=NC(=C(Cl)C(=O)N1)CC)c(OCCC)cc2)N3CCN(C)CC3
SMILES CACTVS 3.370 CCCOc1ccc(cc1C2=NC(=C(Cl)C(=O)N2)CC)[S](=O)(=O)N3CCN(C)CC3
SMILES OpenEye OEToolkits 1.7.2 CCCOc1ccc(cc1C2=NC(=C(C(=O)N2)Cl)CC)S(=O)(=O)N3CCN(CC3)C
Canonical SMILES CACTVS 3.370 CCCOc1ccc(cc1C2=NC(=C(Cl)C(=O)N2)CC)[S](=O)(=O)N3CCN(C)CC3
Canonical SMILES OpenEye OEToolkits 1.7.2 CCCOc1ccc(cc1C2=NC(=C(C(=O)N2)Cl)CC)S(=O)(=O)N3CCN(CC3)C

IUPAC InChI

InChI=1S/C20H27ClN4O4S/c1-4-12-29-17-7-6-14(30(27,28)25-10-8-24(3)9-11-25)13-15(17)19-22-16(5-2)18(21)20(26)23-19/h6-7,13H,4-5,8-12H2,1-3H3,(H,22,23,26)

IUPAC InChI key

HVJOKVUJWQTZFF-UHFFFAOYSA-N
5CO

wwPDB Information

Atom count

57 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-07-06

Last modified at

2011-08-19

Status

Released

Obsoleted

Not Assigned



5CO : Atoms of Molecule

Total Number of Atoms: 57
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CAA C CAA N N N 0 -3.741 5.629 0.831
2 CAB C CAB N N N 0 -5.524 -0.027 2.013
3 CAC C CAC N N N 0 7.306 -1.554 2.239
4 OAD O OAD N N N 0 -2.554 -3.83 -0.58
5 OAE O OAE N N N 0 3.003 -1.021 -2.011
6 OAF O OAF N N N 0 3.936 1.297 -1.93
7 CLAG CL CLAG N N N 0 -5.338 -3.151 0.113
8 CAH C CAH N Y N 0 1.455 2.2 -0.718
9 CAI C CAI N Y N 0 0.212 2.703 -0.386
10 CAJ C CAJ N Y N 0 0.564 -0.023 -0.796
11 CAK C CAK N N N 0 -3.634 4.117 0.624
12 CAL C CAL N N N 0 -5.426 -0.172 0.493
13 CAM C CAM N N N 0 -2.192 3.752 0.265
14 CAN C CAN N N N 0 5.29 -2.006 0.975
15 CAO C CAO N N N 0 6.195 0.243 1.054
16 CAP C CAP N N N 0 3.882 -1.482 0.676
17 CAQ C CAQ N N N 0 4.824 0.859 0.758
18 NAR N NAR N N N 0 -3.027 0.035 -0.005
19 NAS N NAS N N N 0 -1.657 -1.784 -0.526
20 OAT O OAT N N N 0 -2.092 2.34 0.072
21 CAU C CAU N Y N 0 1.63 0.841 -0.923
22 CAV C CAV N Y N 0 -0.871 1.847 -0.255
23 CAW C CAW N N N 0 -4.087 -0.76 0.129
24 CAX C CAX N N N 0 -3.963 -2.105 -0.061
25 CAY C CAY N Y N 0 -0.698 0.472 -0.46
26 CAZ C CAZ N N N 0 -1.843 -0.448 -0.322
27 CBA C CBA N N N 0 -2.701 -2.632 -0.402
28 NBB N NBB N N N 0 6.015 -1.018 1.786
29 NBC N NBC N N N 0 3.999 -0.146 0.071
30 SBD S SBD N N N 0 3.222 0.216 -1.346
31 HAA H HAA N N N 0 -3.453 6.143 -0.086
32 HAAA H HAAA N N N 0 -4.768 5.889 1.087
33 HAAB H HAAB N N N 0 -3.077 5.932 1.641
34 HAB H HAB N N N 0 -4.73 0.63 2.368
35 HABA H HABA N N N 0 -6.492 0.398 2.276
36 HABB H HABB N N N 0 -5.419 -1.008 2.478
37 HAC H HAC N N N 0 7.916 -1.811 1.373
38 HACA H HACA N N N 0 7.821 -0.802 2.836
39 HACB H HACB N N N 0 7.137 -2.445 2.842
40 HAH H HAH N N N 0 2.295 2.871 -0.824
41 HAI H HAI N N N 0 0.084 3.763 -0.229
42 HAJ H HAJ N N N 0 0.705 -1.082 -0.957
43 HAK H HAK N N N 0 -3.921 3.603 1.541
44 HAKA H HAKA N N N 0 -4.298 3.814 -0.186
45 HAL H HAL N N N 0 -6.22 -0.829 0.139
46 HALA H HALA N N N 0 -5.531 0.808 0.028
47 HAM H HAM N N N 0 -1.905 4.266 -0.652
48 HAMA H HAMA N N N 0 -1.528 4.055 1.075
49 HAN H HAN N N N 0 5.22 -2.945 1.523
50 HANA H HANA N N N 0 5.824 -2.17 0.039
51 HAO H HAO N N N 0 6.716 0.048 0.116
52 HAOA H HAOA N N N 0 6.782 0.934 1.659
53 HAP H HAP N N N 0 3.38 -2.156 -0.018
54 HAPA H HAPA N N N 0 3.311 -1.416 1.603
55 HAQ H HAQ N N N 0 4.344 1.15 1.692
56 HAQA H HAQA N N N 0 4.945 1.732 0.118
57 HNAS H HNAS N N N 0 -0.779 -2.124 -0.76



5CO : Chemical Bonds

Total Number of Bonds: 59
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAA CAK C C sing 1.53 N N
2 CAB CAL C C sing 1.53 N N
3 CAC NBB C N sing 1.47 N N
4 OAD CBA O C doub 1.22 N N
5 OAE SBD O S doub 1.42 N N
6 OAF SBD O S doub 1.42 N N
7 CLAG CAX CL C sing 1.74 N N
8 CAH CAI C C doub 1.38 N Y
9 CAH CAU C C sing 1.39 N Y
10 CAI CAV C C sing 1.39 N Y
11 CAJ CAU C C doub 1.38 N Y
12 CAJ CAY C C sing 1.4 N Y
13 CAK CAM C C sing 1.53 N N
14 CAL CAW C C sing 1.51 N N
15 CAM OAT C O sing 1.43 N N
16 CAN CAP C C sing 1.53 N N
17 CAN NBB C N sing 1.47 N N
18 CAO CAQ C C sing 1.53 N N
19 CAO NBB C N sing 1.47 N N
20 CAP NBC C N sing 1.47 N N
21 CAQ NBC C N sing 1.47 N N
22 NAR CAW N C sing 1.33 N N
23 NAR CAZ N C doub 1.32 N N
24 NAS CAZ N C sing 1.36 N N
25 NAS CBA N C sing 1.35 N N
26 OAT CAV O C sing 1.36 N N
27 CAU SBD C S sing 1.76 N N
28 CAV CAY C C doub 1.4 N Y
29 CAW CAX C C doub 1.36 N N
30 CAX CBA C C sing 1.41 N N
31 CAY CAZ C C sing 1.48 N N
32 NBC SBD N S sing 1.66 N N
33 CAA HAA C H sing 1.09 N N
34 CAA HAAA C H sing 1.09 N N
35 CAA HAAB C H sing 1.09 N N
36 CAB HAB C H sing 1.09 N N
37 CAB HABA C H sing 1.09 N N
38 CAB HABB C H sing 1.09 N N
39 CAC HAC C H sing 1.09 N N
40 CAC HACA C H sing 1.09 N N
41 CAC HACB C H sing 1.09 N N
42 CAH HAH C H sing 1.08 N N
43 CAI HAI C H sing 1.08 N N
44 CAJ HAJ C H sing 1.08 N N
45 CAK HAK C H sing 1.09 N N
46 CAK HAKA C H sing 1.09 N N
47 CAL HAL C H sing 1.09 N N
48 CAL HALA C H sing 1.09 N N
49 CAM HAM C H sing 1.09 N N
50 CAM HAMA C H sing 1.09 N N
51 CAN HAN C H sing 1.09 N N
52 CAN HANA C H sing 1.09 N N
53 CAO HAO C H sing 1.09 N N
54 CAO HAOA C H sing 1.09 N N
55 CAP HAP C H sing 1.09 N N
56 CAP HAPA C H sing 1.09 N N
57 CAQ HAQ C H sing 1.09 N N
58 CAQ HAQA C H sing 1.09 N N
59 NAS HNAS N H sing 0.97 N N



5CO : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
5CO 3shz Open in New Window Bound ligand 1 1