Chemical Components in the PDB

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LDR : Summary

Code

LDR

One-letter code

X

Molecule name

phenanthridin-6(5H)-one

Systematic names

ProgramVersionName
ACDLabs 12.01 phenanthridin-6(5H)-one
OpenEye OEToolkits 1.7.2 5H-phenanthridin-6-one

Formula

C13 H9 N O

Formal charge

0

Molecular weight

195.217 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C2c3c(c1c(cccc1)N2)cccc3
SMILES CACTVS 3.370 O=C1Nc2ccccc2c3ccccc13
SMILES OpenEye OEToolkits 1.7.2 c1ccc2c(c1)-c3ccccc3NC2=O
Canonical SMILES CACTVS 3.370 O=C1Nc2ccccc2c3ccccc13
Canonical SMILES OpenEye OEToolkits 1.7.2 c1ccc2c(c1)-c3ccccc3NC2=O

IUPAC InChI

InChI=1S/C13H9NO/c15-13-11-7-2-1-5-9(11)10-6-3-4-8-12(10)14-13/h1-8H,(H,14,15)

IUPAC InChI key

RZFVLEJOHSLEFR-UHFFFAOYSA-N
LDR

wwPDB Information

Atom count

24 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-06-14

Last modified at

2011-07-01

Status

Released

Obsoleted

Not Assigned



LDR : 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 OAA O OAA N N N 0 -1.418 -2.777 0.011
2 CAB C CAB N Y N 0 3.628 0.202 -0.001
3 CAC C CAC N Y N 0 -3.35 0.932 -0.004
4 CAD C CAD N Y N 0 3.089 1.479 0.004
5 CAE C CAE N Y N 0 -2.556 2.069 0.002
6 CAF C CAF N Y N 0 2.807 -0.906 -0.006
7 CAG C CAG N Y N 0 -2.779 -0.323 -0.002
8 CAH C CAH N Y N 0 1.722 1.655 0.004
9 CAI C CAI N Y N 0 -1.18 1.965 0.003
10 NAJ N NAJ N N N 0 0.602 -1.864 -0.004
11 CAK C CAK N N N 0 -0.739 -1.768 0.0
12 CAL C CAL N Y N 0 1.424 -0.749 0.0
13 CAM C CAM N Y N 0 -1.391 -0.449 -0.007
14 CAN C CAN N Y N 0 0.88 0.544 -0.001
15 CAO C CAO N Y N 0 -0.586 0.709 -0.002
16 HAB H HAB N N N 0 4.7 0.073 -0.005
17 HAC H HAC N N N 0 -4.425 1.03 -0.009
18 HAD H HAD N N N 0 3.743 2.339 0.008
19 HAE H HAE N N N 0 -3.019 3.045 0.0
20 HAF H HAF N N N 0 3.237 -1.896 -0.014
21 HAG H HAG N N N 0 -3.404 -1.204 -0.006
22 HAH H HAH N N N 0 1.304 2.651 0.009
23 HAI H HAI N N N 0 -0.568 2.855 0.007
24 HNAJ H HNAJ N N N 0 1.008 -2.745 0.001



LDR : 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 CAK OAA C O doub 1.22 N N
2 CAD CAB C C doub 1.39 N Y
3 CAB CAF C C sing 1.38 N Y
4 CAB HAB C H sing 1.08 N N
5 CAE CAC C C doub 1.39 N Y
6 CAC CAG C C sing 1.38 N Y
7 CAC HAC C H sing 1.08 N N
8 CAD CAH C C sing 1.38 N Y
9 CAD HAD C H sing 1.08 N N
10 CAI CAE C C sing 1.38 N Y
11 CAE HAE C H sing 1.08 N N
12 CAF CAL C C doub 1.39 N Y
13 CAF HAF C H sing 1.08 N N
14 CAM CAG C C doub 1.39 N Y
15 CAG HAG C H sing 1.08 N N
16 CAH CAN C C doub 1.39 N Y
17 CAH HAH C H sing 1.08 N N
18 CAI CAO C C doub 1.39 N Y
19 CAI HAI C H sing 1.08 N N
20 CAL NAJ C N sing 1.39 N N
21 NAJ CAK N C sing 1.34 N N
22 NAJ HNAJ N H sing 0.97 N N
23 CAM CAK C C sing 1.47 N N
24 CAN CAL C C sing 1.4 N Y
25 CAO CAM C C sing 1.41 N Y
26 CAN CAO C C sing 1.48 N N



LDR : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
LDR 3se2 Open in New Window Bound ligand 2 1
LDR 4avu Open in New Window Bound ligand 2 1
LDR 5xhk Open in New Window Bound ligand 1 1
LDR 7enz Open in New Window Bound ligand 1 1