Chemical Components in the PDB

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UBA : Summary

Code

UBA

One-letter code

X

Molecule name

(S)-1-(2-AMINO-2-CARBOXYETHYL)-3(2-CARBOXYTHIOPHENE-3-YL-METHYL)-5-METHYLPYRIMIDINE-2,4-DIONE

Systematic names

ProgramVersionName
ACDLabs 10.04 3-({3-[(2S)-2-amino-2-carboxyethyl]-5-methyl-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)thiophene-2-carboxylic acid
OpenEye OEToolkits 1.5.0 3-[[3-[(2S)-2-amino-3-hydroxy-3-oxo-propyl]-5-methyl-2,6-dioxo-pyrimidin-1-yl]methyl]thiophene-2-carboxylic acid

Formula

C14 H15 N3 O6 S

Formal charge

0

Molecular weight

353.35 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(N)CN1C(=O)N(C(=O)C(=C1)C)Cc2c(scc2)C(=O)O
SMILES CACTVS 3.341 CC1=CN(C[CH](N)C(O)=O)C(=O)N(Cc2ccsc2C(O)=O)C1=O
SMILES OpenEye OEToolkits 1.5.0 CC1=CN(C(=O)N(C1=O)Cc2ccsc2C(=O)O)CC(C(=O)O)N
Canonical SMILES CACTVS 3.341 CC1=CN(C[C@H](N)C(O)=O)C(=O)N(Cc2ccsc2C(O)=O)C1=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC1=CN(C(=O)N(C1=O)Cc2ccsc2C(=O)O)C[C@@H](C(=O)O)N

IUPAC InChI

InChI=1S/C14H15N3O6S/c1-7-4-16(6-9(15)12(19)20)14(23)17(11(7)18)5-8-2-3-24-10(8)13(21)22/h2-4,9H,5-6,15H2,1H3,(H,19,20)(H,21,22)/t9-/m0/s1

IUPAC InChI key

ZTAZUCRXCRXNSU-VIFPVBQESA-N
UBA

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

2005-12-06

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



UBA : 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 OXT O OXT N N N 0 5.696 -1.582 0.386
2 C C C N N N 0 4.627 -1.898 -0.08
3 O O O N N N 0 4.528 -2.99 -0.854
4 CA C CA S N N 0 3.404 -1.065 0.207
5 N N N N N N 0 3.638 -0.25 1.407
6 CB C CB N N N 0 3.12 -0.148 -0.984
7 N4 N N4 N Y N 0 2.005 0.745 -0.658
8 C5 C C5 N Y N 0 0.744 0.365 -0.934
9 O8 O O8 N N N 0 0.544 -0.717 -1.452
10 N6 N N6 N Y N 0 -0.298 1.165 -0.645
11 C1 C C1 N Y N 0 -0.094 2.366 -0.066
12 O7 O O7 N N N 0 -1.037 3.091 0.195
13 C2 C C2 N Y N 0 1.228 2.78 0.225
14 C6 C C6 N N N 0 1.485 4.119 0.867
15 C3 C C3 N Y N 0 2.256 1.957 -0.075
16 C17 C C17 N N N 0 -1.662 0.728 -0.955
17 C18 C C18 N Y N 0 -2.198 -0.094 0.189
18 C23 C C23 N Y N 0 -1.492 -0.243 1.356
19 C22 C C22 N Y N 0 -2.019 -0.995 2.359
20 S20 S S20 N Y N 0 -3.533 -1.525 1.703
21 C19 C C19 N Y N 0 -3.429 -0.728 0.11
22 C10 C C10 N N N 0 -4.39 -0.744 -0.994
23 O2 O O2 N N N 0 -5.588 -1.345 -0.838
24 O1 O O1 N N N 0 -4.108 -0.216 -2.053
25 HO H HO N N N 0 5.312 -3.525 -1.039
26 HA H HA N N N 0 2.549 -1.72 0.374
27 HN1 H 1HN N N N 0 3.922 -0.885 2.138
28 HN2 H 2HN N N N 0 4.434 0.337 1.208
29 HB1 H 1HB N N N 0 2.859 -0.752 -1.853
30 HB2 H 2HB N N N 0 4.007 0.445 -1.206
31 H61 H 1H6 N N N 0 1.621 4.873 0.093
32 H62 H 2H6 N N N 0 0.635 4.39 1.494
33 H63 H 3H6 N N N 0 2.384 4.061 1.481
34 H3 H H3 N N N 0 3.271 2.254 0.143
35 H171 H 1H17 N N N 0 -2.298 1.6 -1.105
36 H172 H 2H17 N N N 0 -1.652 0.124 -1.863
37 H23 H H23 N N N 0 -0.529 0.23 1.476
38 H22 H H22 N N N 0 -1.596 -1.21 3.329
39 HO2 H HO2 N N N 0 -6.222 -1.355 -1.568



UBA : 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 OXT C O C doub 1.21 N N
2 C O C O sing 1.34 N N
3 C CA C C sing 1.51 N N
4 O HO O H sing 0.97 N N
5 CA N C N sing 1.47 N N
6 CA CB C C sing 1.53 N N
7 CA HA C H sing 1.09 N N
8 N HN1 N H sing 1.01 N N
9 N HN2 N H sing 1.01 N N
10 CB N4 C N sing 1.47 N N
11 CB HB1 C H sing 1.09 N N
12 CB HB2 C H sing 1.09 N N
13 N4 C5 N C sing 1.35 N Y
14 N4 C3 N C sing 1.37 N Y
15 C5 O8 C O doub 1.22 N N
16 C5 N6 C N sing 1.35 N Y
17 N6 C1 N C sing 1.35 N Y
18 N6 C17 N C sing 1.47 N N
19 C1 O7 C O doub 1.22 N N
20 C1 C2 C C sing 1.42 N Y
21 C2 C6 C C sing 1.51 N N
22 C2 C3 C C doub 1.35 N Y
23 C6 H61 C H sing 1.09 N N
24 C6 H62 C H sing 1.09 N N
25 C6 H63 C H sing 1.09 N N
26 C3 H3 C H sing 1.08 N N
27 C17 C18 C C sing 1.51 N N
28 C17 H171 C H sing 1.09 N N
29 C17 H172 C H sing 1.09 N N
30 C18 C23 C C sing 1.37 N Y
31 C18 C19 C C doub 1.39 N Y
32 C23 C22 C C doub 1.36 N Y
33 C23 H23 C H sing 1.08 N N
34 C22 S20 C S sing 1.73 N Y
35 C22 H22 C H sing 1.08 N N
36 S20 C19 S C sing 1.78 N Y
37 C19 C10 C C sing 1.46 N N
38 C10 O2 C O sing 1.35 N N
39 C10 O1 C O doub 1.22 N N
40 O2 HO2 O H sing 0.97 N N



UBA : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
UBA 2f34 Open in New Window Bound ligand 2 1
UBA 2ojt Open in New Window Bound ligand 2 1