Chemical Components in the PDB

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UBC : Summary

Code

UBC

One-letter code

X

Molecule name

(S)-1-(2-AMINO-2-CARBOXYETHYL)-3-(2-CARBOXYBENZYL)PYRIMIDINE-2,4-DIONE

Systematic names

ProgramVersionName
ACDLabs 10.04 2-({3-[(2S)-2-amino-2-carboxyethyl]-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)benzoic acid
OpenEye OEToolkits 1.5.0 2-[[3-[(2S)-2-amino-3-hydroxy-3-oxo-propyl]-2,6-dioxo-pyrimidin-1-yl]methyl]benzoic acid

Formula

C15 H15 N3 O6

Formal charge

0

Molecular weight

333.296 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)c1ccccc1CN2C(=O)C=CN(C2=O)CC(N)C(=O)O
SMILES CACTVS 3.341 N[CH](CN1C=CC(=O)N(Cc2ccccc2C(O)=O)C1=O)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 c1ccc(c(c1)CN2C(=O)C=CN(C2=O)CC(C(=O)O)N)C(=O)O
Canonical SMILES CACTVS 3.341 N[C@@H](CN1C=CC(=O)N(Cc2ccccc2C(O)=O)C1=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1ccc(c(c1)CN2C(=O)C=CN(C2=O)C[C@@H](C(=O)O)N)C(=O)O

IUPAC InChI

InChI=1S/C15H15N3O6/c16-11(14(22)23)8-17-6-5-12(19)18(15(17)24)7-9-3-1-2-4-10(9)13(20)21/h1-6,11H,7-8,16H2,(H,20,21)(H,22,23)/t11-/m0/s1

IUPAC InChI key

UUIYULWYHDSXHL-NSHDSACASA-N
UBC

wwPDB Information

Atom count

39 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2005-12-07

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



UBC : Atoms of Molecule

Total Number of Atoms: 39
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 5.156 -1.245 -0.173
2 C1 C C1 N Y N 0 -0.222 2.047 0.672
3 C10 C C10 N N N 0 -4.147 -1.189 1.123
4 C17 C C17 N N N 0 -1.518 -0.0030 0.894
5 C2 C C2 N Y N 0 0.969 2.724 0.318
6 C21 C C21 N Y N 0 -2.465 -0.0020 -0.278
7 C22 C C22 N Y N 0 -3.73 -0.58 -0.156
8 C23 C C23 N Y N 0 -4.604 -0.569 -1.246
9 C24 C C24 N Y N 0 -4.208 0.0010 -2.437
10 C25 C C25 N Y N 0 -2.95 0.567 -2.553
11 C26 C C26 N Y N 0 -2.082 0.565 -1.477
12 C3 C C3 N Y N 0 2.014 2.012 -0.156
13 C5 C C5 N Y N 0 0.764 0.023 0.05
14 CA C CA S N N 0 3.928 -0.557 0.364
15 CB C CB N N N 0 3.037 -0.119 -0.801
16 H171 H 1H17 N N N 0 -1.276 -1.031 1.164
17 H172 H 2H17 N N N 0 -1.989 0.495 1.742
18 H2 H H2 N N N 0 1.042 3.796 0.425
19 H23 H H23 N N N 0 -5.586 -1.011 -1.156
20 H24 H H24 N N N 0 -4.881 0.0060 -3.282
21 H25 H H25 N N N 0 -2.646 1.013 -3.489
22 H26 H H26 N N N 0 -1.102 1.008 -1.574
23 H3 H H3 N N N 0 2.931 2.511 -0.432
24 HA H HA N N N 0 3.376 -1.245 1.005
25 HB1 H 1HB N N N 0 3.616 0.497 -1.488
26 HB2 H 2HB N N N 0 2.667 -1.0 -1.326
27 HN1 H 1HN N N N 0 4.833 1.228 0.513
28 HN2 H 2HN N N N 0 3.48 1.107 1.394
29 HO H HO N N N 0 5.878 -2.971 -0.905
30 HO1 H HO1 N N N 0 -5.596 -2.239 2.045
31 N N N N N N 0 4.329 0.622 1.143
32 N4 N N4 N Y N 0 1.904 0.654 -0.286
33 N6 N N6 N Y N 0 -0.29 0.708 0.53
34 O O O N N N 0 5.09 -2.529 -0.561
35 O1 O O1 N N N 0 -5.324 -1.84 1.208
36 O2 O O2 N N N 0 -3.429 -1.104 2.099
37 O7 O O7 N N N 0 -1.178 2.669 1.102
38 O8 O O8 N N N 0 0.689 -1.184 -0.073
39 OXT O OXT N N N 0 6.199 -0.642 -0.255



UBC : Chemical Bonds

Total Number of Bonds: 40
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1 C10 O C sing 1.35 N N
2 O1 HO1 O H sing 0.97 N N
3 C10 O2 C O doub 1.21 N N
4 C10 C22 C C sing 1.48 N N
5 C22 C23 C C doub 1.4 N Y
6 C22 C21 C C sing 1.4 N Y
7 C23 C24 C C sing 1.38 N Y
8 C23 H23 C H sing 1.08 N N
9 C24 C25 C C doub 1.38 N Y
10 C24 H24 C H sing 1.08 N N
11 C25 C26 C C sing 1.38 N Y
12 C25 H25 C H sing 1.08 N N
13 C26 C21 C C doub 1.38 N Y
14 C26 H26 C H sing 1.08 N N
15 C21 C17 C C sing 1.51 N N
16 C17 N6 C N sing 1.46 N N
17 C17 H171 C H sing 1.09 N N
18 C17 H172 C H sing 1.09 N N
19 N6 C5 N C sing 1.35 N Y
20 N6 C1 N C sing 1.35 N Y
21 C5 O8 C O doub 1.22 N N
22 C5 N4 C N sing 1.35 N Y
23 C1 O7 C O doub 1.22 N N
24 C1 C2 C C sing 1.41 N Y
25 C2 C3 C C doub 1.35 N Y
26 C2 H2 C H sing 1.08 N N
27 C3 N4 C N sing 1.37 N Y
28 C3 H3 C H sing 1.08 N N
29 N4 CB N C sing 1.47 N N
30 CB CA C C sing 1.53 N N
31 CB HB1 C H sing 1.09 N N
32 CB HB2 C H sing 1.09 N N
33 CA N C N sing 1.47 N N
34 CA C C C sing 1.51 N N
35 CA HA C H sing 1.09 N N
36 N HN1 N H sing 1.01 N N
37 N HN2 N H sing 1.01 N N
38 C O C O sing 1.34 N N
39 C OXT C O doub 1.21 N N
40 O HO O H sing 0.97 N N



UBC : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
UBC 2f35 Open in New Window Bound ligand 2 1