Chemical Components in the PDB

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4WF : Summary

Code

4WF

One-letter code

X

Molecule name

5-azanyl-6-oxidanyl-1-(phenylmethyl)pyrimidine-2,4-dione

Systematic names

ProgramVersionName
ACDLabs 12.01 5-amino-1-benzyl-6-hydroxypyrimidine-2,4(1H,3H)-dione
OpenEye OEToolkits 1.9.2 5-azanyl-6-oxidanyl-1-(phenylmethyl)pyrimidine-2,4-dione

Formula

C11 H11 N3 O3

Formal charge

0

Molecular weight

233.223 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1C(=C(O)N(C(=O)N1)Cc2ccccc2)N
SMILES CACTVS 3.385 NC1=C(O)N(Cc2ccccc2)C(=O)NC1=O
SMILES OpenEye OEToolkits 1.9.2 c1ccc(cc1)CN2C(=C(C(=O)NC2=O)N)O
Canonical SMILES CACTVS 3.385 NC1=C(O)N(Cc2ccccc2)C(=O)NC1=O
Canonical SMILES OpenEye OEToolkits 1.9.2 c1ccc(cc1)CN2C(=C(C(=O)NC2=O)N)O

IUPAC InChI

InChI=1S/C11H11N3O3/c12-8-9(15)13-11(17)14(10(8)16)6-7-4-2-1-3-5-7/h1-5,16H,6,12H2,(H,13,15,17)

IUPAC InChI key

HTIBHRPLOZXHDY-UHFFFAOYSA-N
4WF

wwPDB Information

Atom count

28 (17 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-04-27

Last modified at

2014-09-05

Status

Released

Obsoleted

Not Assigned



4WF : Atoms of Molecule

Total Number of Atoms: 28
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C N N N 0 1.125 -0.893 -0.501
2 CA C CA N N N 0 2.302 -0.807 0.184
3 CA0 C CA0 N N N 0 0.878 1.452 -0.373
4 CAE C CAE N Y N 0 -4.08 -0.312 1.226
5 CAF C CAF N Y N 0 -3.674 0.955 0.852
6 CAG C CAG N Y N 0 -3.437 -1.423 0.714
7 CAH C CAH N Y N 0 -2.626 1.111 -0.036
8 CAI C CAI N Y N 0 -2.389 -1.267 -0.175
9 CAJ C CAJ N N N 0 -0.842 0.17 -1.519
10 CAQ C CAQ N Y N 0 -1.984 0.0 -0.55
11 CB C CB N N N 0 2.761 0.46 0.597
12 HAB H HAB N N N 0 2.347 2.43 0.591
13 HAE H HAE N N N 0 -4.895 -0.434 1.923
14 HAF H HAF N N N 0 -4.177 1.823 1.252
15 HAG H HAG N N N 0 -3.753 -2.413 1.007
16 HAH H HAH N N N 0 -2.31 2.102 -0.329
17 HAI H HAI N N N 0 -1.887 -2.135 -0.576
18 HAJ1 H HAJ1 N N N 0 -0.987 1.085 -2.093
19 HAJ2 H HAJ2 N N N 0 -0.811 -0.683 -2.196
20 HN1 H HN1 N N N 0 2.727 -2.839 0.187
21 HN2 H HN2 N N N 0 3.885 -1.901 0.962
22 HO H HO N N N 0 1.23 -2.839 -0.67
23 N N N N N N 0 3.05 -1.97 0.475
24 NAB N NAB N N N 0 2.033 1.557 0.309
25 NAL N NAL N N N 0 0.419 0.254 -0.778
26 O O O N N N 0 0.66 -2.096 -0.91
27 OAC O OAC N N N 0 0.237 2.454 -0.623
28 OAN O OAN N N N 0 3.81 0.563 1.21



4WF : Chemical Bonds

Total Number of Bonds: 29
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C O C O sing 1.3530391 N N
2 O HO O H sing 0.96672076 N N
3 C CA C C doub 1.3645328 N N
4 C NAL C N sing 1.3750542 N N
5 N CA N C sing 1.4130654 N N
6 CA CB C C sing 1.4094464 N N
7 CB OAN C O doub 1.2193354 N N
8 CB NAB C N sing 1.3477155 N N
9 OAC CA0 O C doub 1.2154772 N N
10 CAE CAF C C sing 1.3820279 N Y
11 CAE CAG C C doub 1.3819964 N Y
12 CAF CAH C C doub 1.3824558 N Y
13 CAG CAI C C sing 1.3830984 N Y
14 CAH CAQ C C sing 1.3822738 N Y
15 CAI CAQ C C doub 1.3820055 N Y
16 CAJ NAL C N sing 1.4650112 N N
17 CAJ CAQ C C sing 1.5073237 N N
18 NAL CA0 N C sing 1.3453289 N N
19 CA0 NAB C N sing 1.345427 N N
20 N HN1 N H sing 0.9707904 N N
21 N HN2 N H sing 0.9691001 N N
22 NAB HAB N H sing 0.9696644 N N
23 CAE HAE C H sing 1.0793136 N N
24 CAF HAF C H sing 1.0800153 N N
25 CAG HAG C H sing 1.0797246 N N
26 CAH HAH C H sing 1.0806415 N N
27 CAI HAI C H sing 1.0799209 N N
28 CAJ HAJ1 C H sing 1.0898284 N N
29 CAJ HAJ2 C H sing 1.0894489 N N



4WF : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
4WF 3zll Open in New Window Bound ligand 4 1