Chemical Components in the PDB

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LRO : Summary

Code

LRO

One-letter code

X

Molecule name

5-[2-(4-methylphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 5-[2-(4-methylphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
OpenEye OEToolkits 1.7.6 5-[2-(4-methylphenyl)ethyl]-2,4-bis(oxidanylidene)-1H-pyrimidine-6-carboxylic acid

Formula

C14 H14 N2 O4

Formal charge

0

Molecular weight

274.272 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1NC(C(=O)O)=C(C(=O)N1)CCc2ccc(cc2)C
SMILES CACTVS 3.370 Cc1ccc(CCC2=C(NC(=O)NC2=O)C(O)=O)cc1
SMILES OpenEye OEToolkits 1.7.6 Cc1ccc(cc1)CCC2=C(NC(=O)NC2=O)C(=O)O
Canonical SMILES CACTVS 3.370 Cc1ccc(CCC2=C(NC(=O)NC2=O)C(O)=O)cc1
Canonical SMILES OpenEye OEToolkits 1.7.6 Cc1ccc(cc1)CCC2=C(NC(=O)NC2=O)C(=O)O

IUPAC InChI

InChI=1S/C14H14N2O4/c1-8-2-4-9(5-3-8)6-7-10-11(13(18)19)15-14(20)16-12(10)17/h2-5H,6-7H2,1H3,(H,18,19)(H2,15,16,17,20)

IUPAC InChI key

BBNOPYKTLSUCSO-UHFFFAOYSA-N
LRO

wwPDB Information

Atom count

34 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-11-27

Last modified at

2013-11-22

Status

Released

Obsoleted

Not Assigned



LRO : Atoms of Molecule

Total Number of Atoms: 34
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OAB O OAB N N N 0 -2.273 -3.196 0.111
2 CAN C CAN N N N 0 -1.515 -2.086 0.179
3 CAS C CAS N N N 0 -4.098 0.571 -0.185
4 OAE O OAE N N N 0 -0.31 -2.179 0.289
5 CAQ C CAQ N N N 0 -2.152 -0.748 0.12
6 NAL N NAL N N N 0 -3.503 -0.632 -0.128
7 OAC O OAC N N N 0 -5.292 0.63 -0.407
8 NAM N NAM N N N 0 -3.409 1.711 -0.004
9 OAD O OAD N N N 0 -1.457 2.706 0.409
10 CAT C CAT N N N 0 -2.083 1.676 0.244
11 CAR C CAR N N N 0 -1.411 0.373 0.316
12 CAK C CAK N N N 0 0.068 0.283 0.59
13 CAJ C CAJ N N N 0 0.837 0.357 -0.73
14 CAP C CAP N Y N 0 2.317 0.266 -0.456
15 CAH C CAH N Y N 0 2.94 -0.967 -0.429
16 CAF C CAF N Y N 0 4.297 -1.05 -0.177
17 CAO C CAO N Y N 0 5.03 0.1 0.048
18 CAA C CAA N N N 0 6.509 0.009 0.323
19 CAG C CAG N Y N 0 4.406 1.334 0.02
20 CAI C CAI N Y N 0 3.051 1.417 -0.237
21 H1 H H1 N N N 0 -1.813 -4.046 0.154
22 H2 H H2 N N N 0 -3.868 2.564 -0.052
23 H7 H H7 N N N 0 0.617 1.302 -1.226
24 H4 H H4 N N N 0 0.37 1.11 1.233
25 H5 H H5 N N N 0 0.289 -0.662 1.086
26 H6 H H6 N N N 0 0.536 -0.47 -1.373
27 H8 H H8 N N N 0 2.368 -1.866 -0.605
28 H9 H H9 N N N 0 4.784 -2.014 -0.156
29 H10 H H10 N N N 0 7.057 0.062 -0.617
30 H11 H H11 N N N 0 6.81 0.836 0.966
31 H12 H H12 N N N 0 6.729 -0.936 0.819
32 H13 H H13 N N N 0 4.979 2.232 0.196
33 H14 H H14 N N N 0 2.564 2.381 -0.259
34 H15 H H15 N N N 0 -4.033 -1.433 -0.264



LRO : Chemical Bonds

Total Number of Bonds: 35
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAG CAO C C doub 1.38 N Y
2 CAG CAI C C sing 1.38 N Y
3 CAA CAO C C sing 1.51 N N
4 CAO CAF C C sing 1.38 N Y
5 CAI CAP C C doub 1.38 N Y
6 CAP CAH C C sing 1.38 N Y
7 CAP CAJ C C sing 1.51 N N
8 CAF CAH C C doub 1.38 N Y
9 CAJ CAK C C sing 1.53 N N
10 CAK CAR C C sing 1.51 N N
11 OAD CAT O C doub 1.22 N N
12 CAR CAT C C sing 1.47 N N
13 CAR CAQ C C doub 1.36 N N
14 CAT NAM C N sing 1.35 N N
15 OAE CAN O C doub 1.21 N N
16 CAN CAQ C C sing 1.48 N N
17 CAN OAB C O sing 1.35 N N
18 CAQ NAL C N sing 1.38 N N
19 NAM CAS N C sing 1.34 N N
20 NAL CAS N C sing 1.34 N N
21 CAS OAC C O doub 1.22 N N
22 OAB H1 O H sing 0.97 N N
23 NAM H2 N H sing 0.97 N N
24 CAK H4 C H sing 1.09 N N
25 CAK H5 C H sing 1.09 N N
26 CAJ H6 C H sing 1.09 N N
27 CAJ H7 C H sing 1.09 N N
28 CAH H8 C H sing 1.08 N N
29 CAF H9 C H sing 1.08 N N
30 CAA H10 C H sing 1.09 N N
31 CAA H11 C H sing 1.09 N N
32 CAA H12 C H sing 1.09 N N
33 CAG H13 C H sing 1.08 N N
34 CAI H14 C H sing 1.08 N N
35 NAL H15 N H sing 0.97 N N



LRO : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
LRO 3w1u Open in New Window Bound ligand 2 1