Chemical Components in the PDB

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FDR : Summary

Code

FDR

One-letter code

X

Molecule name

2-methyl-3,5,6,7-tetrahydro-4H-cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-one

Systematic names

ProgramVersionName
ACDLabs 12.01 2-methyl-3,5,6,7-tetrahydro-4H-cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-one

Formula

C10 H10 N2 O S

Formal charge

0

Molecular weight

206.264 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1c2c3c(sc2N=C(N1)C)CCC3
SMILES CACTVS 3.370 CC1=Nc2sc3CCCc3c2C(=O)N1
SMILES OpenEye OEToolkits 1.7.2 CC1=Nc2c(c3c(s2)CCC3)C(=O)N1
Canonical SMILES CACTVS 3.370 CC1=Nc2sc3CCCc3c2C(=O)N1
Canonical SMILES OpenEye OEToolkits 1.7.2 CC1=Nc2c(c3c(s2)CCC3)C(=O)N1

IUPAC InChI

InChI=1S/C10H10N2OS/c1-5-11-9(13)8-6-3-2-4-7(6)14-10(8)12-5/h2-4H2,1H3,(H,11,12,13)

IUPAC InChI key

SSAMSKJKRMKXFV-UHFFFAOYSA-N
FDR

wwPDB Information

Atom count

24 (14 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-06-29

Last modified at

2011-07-15

Status

Released

Obsoleted

Not Assigned



FDR : Atoms of Molecule

Total Number of Atoms: 24
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 4.273 0.52 -0.071
2 OAB O OAB N N N 0 0.747 -2.587 0.054
3 CAC C CAC N N N 0 -3.676 -0.898 -0.326
4 CAD C CAD N N N 0 -3.437 0.565 0.096
5 CAE C CAE N N N 0 -2.355 -1.565 0.105
6 NAF N NAF N N N 0 1.942 1.173 -0.03
7 NAG N NAG N N N 0 2.414 -1.103 -0.006
8 SAH S SAH N Y N 0 -0.749 2.055 0.016
9 CAI C CAI N N N 0 2.802 0.198 -0.033
10 CAJ C CAJ N Y N 0 -1.921 0.739 0.061
11 CAK C CAK N Y N 0 -1.317 -0.444 0.066
12 CAL C CAL N N N 0 1.104 -1.422 0.028
13 CAM C CAM N Y N 0 0.61 0.941 0.004
14 CAN C CAN N Y N 0 0.144 -0.363 0.034
15 HAA H HAA N N N 0 4.408 1.602 -0.092
16 HAAA H HAAA N N N 0 4.758 0.111 0.815
17 HAAB H HAAB N N N 0 4.718 0.082 -0.965
18 HAC H HAC N N N 0 -4.523 -1.326 0.21
19 HACA H HACA N N N 0 -3.819 -0.975 -1.404
20 HAD H HAD N N N 0 -3.913 1.246 -0.61
21 HADA H HADA N N N 0 -3.817 0.737 1.103
22 HAE H HAE N N N 0 -2.444 -1.965 1.115
23 HAEA H HAEA N N N 0 -2.085 -2.358 -0.593
24 HNAG H HNAG N N N 0 3.082 -1.806 -0.01



FDR : Chemical Bonds

Total Number of Bonds: 26
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAA CAI C C sing 1.51 N N
2 CAA HAA C H sing 1.09 N N
3 CAA HAAA C H sing 1.09 N N
4 CAA HAAB C H sing 1.09 N N
5 CAL OAB C O doub 1.22 N N
6 CAE CAC C C sing 1.54 N N
7 CAD CAC C C sing 1.54 N N
8 CAC HAC C H sing 1.09 N N
9 CAC HACA C H sing 1.09 N N
10 CAJ CAD C C sing 1.53 N N
11 CAD HAD C H sing 1.09 N N
12 CAD HADA C H sing 1.09 N N
13 CAK CAE C C sing 1.53 N N
14 CAE HAE C H sing 1.09 N N
15 CAE HAEA C H sing 1.09 N N
16 CAI NAF C N doub 1.3 N N
17 NAF CAM N C sing 1.35 N N
18 CAI NAG C N sing 1.36 N N
19 NAG CAL N C sing 1.35 N N
20 NAG HNAG N H sing 0.97 N N
21 CAM SAH C S sing 1.76 N Y
22 SAH CAJ S C sing 1.76 N Y
23 CAK CAJ C C doub 1.33 N Y
24 CAN CAK C C sing 1.46 N Y
25 CAL CAN C C sing 1.43 N N
26 CAM CAN C C doub 1.39 N Y



FDR : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
FDR 3smj Open in New Window Bound ligand 2 1
FDR 6we4 Open in New Window Bound ligand 1 1