Chemical Components in the PDB

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URC : Summary

Code

URC

One-letter code

X

Molecule name

URIC ACID

Synonyms

7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE

Systematic names

ProgramVersionName
ACDLabs 10.04 7,9-dihydro-1H-purine-2,6,8(3H)-trione
OpenEye OEToolkits 1.5.0 7,9-dihydro-3H-purine-2,6,8-trione

Formula

C5 H4 N4 O3

Formal charge

0

Molecular weight

168.11 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1C2=C(NC(=O)N1)NC(=O)N2
SMILES CACTVS 3.341 O=C1NC(=O)C2=C(N1)NC(=O)N2
SMILES OpenEye OEToolkits 1.5.0 C12=C(NC(=O)N1)NC(=O)NC2=O
Canonical SMILES CACTVS 3.341 O=C1NC(=O)C2=C(N1)NC(=O)N2
Canonical SMILES OpenEye OEToolkits 1.5.0 C12=C(NC(=O)N1)NC(=O)NC2=O

IUPAC InChI

InChI=1S/C5H4N4O3/c10-3-1-2(7-4(11)6-1)8-5(12)9-3/h(H4,6,7,8,9,10,11,12)

IUPAC InChI key

LEHOTFFKMJEONL-UHFFFAOYSA-N
URC

wwPDB Information

Atom count

16 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2002-03-15

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



URC : Atoms of Molecule

Total Number of Atoms: 16
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C2 N Y N 0 -0.678 -0.0010 -2.078
2 C4 C C4 N Y N 0 -0.804 0.0 0.278
3 C5 C C5 N Y N 0 0.561 0.0 0.347
4 C6 C C6 N Y N 0 1.311 0.0 -0.845
5 C8 C C8 N Y N 0 -0.238 0.0 2.415
6 HN1 H HN1 N N N 0 1.176 0.0 -2.855
7 HN3 H HN3 N N N 0 -2.385 0.0040 -1.011
8 HN7 H HN7 N N N 0 1.806 0.0 2.065
9 HN9 H HN9 N N N 0 -2.218 0.0 1.819
10 N1 N N1 N Y N 0 0.666 0.0 -2.03
11 N3 N N3 N Y N 0 -1.417 0.0040 -0.953
12 N7 N N7 N Y N 0 0.906 0.0 1.703
13 N9 N N9 N Y N 0 -1.282 0.0 1.564
14 O11 O O11 N N N 0 -1.236 -0.0010 -3.159
15 O13 O O13 N N N 0 2.529 0.0 -0.807
16 O24 O O24 N N N 0 -0.316 0.0 3.629



URC : Chemical Bonds

Total Number of Bonds: 17
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C sing 1.34 N Y
2 N1 C6 N C sing 1.35 N Y
3 N1 HN1 N H sing 0.97 N N
4 C2 N3 C N sing 1.35 N Y
5 C2 O11 C O doub 1.22 N N
6 C6 C5 C C sing 1.41 N Y
7 C6 O13 C O doub 1.22 N N
8 N3 C4 N C sing 1.38 N Y
9 N3 HN3 N H sing 0.97 N N
10 C4 C5 C C doub 1.37 N Y
11 C4 N9 C N sing 1.37 N Y
12 C5 N7 C N sing 1.4 N Y
13 N9 C8 N C sing 1.35 N Y
14 N9 HN9 N H sing 0.97 N N
15 N7 C8 N C sing 1.35 N Y
16 N7 HN7 N H sing 0.97 N N
17 C8 O24 C O doub 1.22 N N



URC : Used in PDB Entries

Total Number of PDB Entries: 22
Ligand Code PDB Entry ID Type Total Distinct
URC 1l5s Open in New Window Bound ligand 2 1
URC 2e3t Open in New Window Bound ligand 2 1
URC 2yzb Open in New Window Bound ligand 8 1
URC 3amz Open in New Window Bound ligand 2 1
URC 3an1 Open in New Window Bound ligand 2 1
URC 3bjp Open in New Window Bound ligand 1 1
URC 3l9g Open in New Window Bound ligand 1 1
URC 3obp Open in New Window Bound ligand 1 1
URC 3rp7 Open in New Window Bound ligand 1 1
URC 4d12 Open in New Window Bound ligand 1 1
URC 4d17 Open in New Window Bound ligand 1 1
URC 4d19 Open in New Window Bound ligand 1 1
URC 4pr8 Open in New Window Bound ligand 1 1
URC 4yrw Open in New Window Bound ligand 2 1
URC 4ysw Open in New Window Bound ligand 2 1
URC 4yty Open in New Window Bound ligand 1 1
URC 4ytz Open in New Window Bound ligand 2 1
URC 6a7x Open in New Window Bound ligand 2 1
URC 6abu Open in New Window Bound ligand 2 1
URC 6ac1 Open in New Window Bound ligand 2 1
URC 6ad4 Open in New Window Bound ligand 2 1
URC 6aju Open in New Window Bound ligand 2 1