Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

IBA : Summary

Code

IBA

One-letter code

X

Molecule name

4-[(2R)-2-(AMINOMETHYL)-2-(HYDROXYMETHYL)-5-OXOPYRROLIDIN-1-YL]-3-[(1-ETHYLPROPYL)AMINO]BENZOIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 4-[(2R)-2-(aminomethyl)-2-(hydroxymethyl)-5-oxopyrrolidin-1-yl]-3-[(1-ethylpropyl)amino]benzoic acid
OpenEye OEToolkits 1.5.0 4-[(2R)-2-(aminomethyl)-2-(hydroxymethyl)-5-oxo-pyrrolidin-1-yl]-3-(pentan-3-ylamino)benzoic acid

Formula

C18 H27 N3 O4

Formal charge

0

Molecular weight

349.425 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)c1cc(c(cc1)N2C(=O)CCC2(CN)CO)NC(CC)CC
SMILES CACTVS 3.341 CCC(CC)Nc1cc(ccc1N2C(=O)CC[C]2(CN)CO)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 CCC(CC)Nc1cc(ccc1N2C(=O)CCC2(CN)CO)C(=O)O
Canonical SMILES CACTVS 3.341 CCC(CC)Nc1cc(ccc1N2C(=O)CC[C@@]2(CN)CO)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CCC(CC)Nc1cc(ccc1N2C(=O)CC[C@@]2(CN)CO)C(=O)O

IUPAC InChI

InChI=1S/C18H27N3O4/c1-3-13(4-2)20-14-9-12(17(24)25)5-6-15(14)21-16(23)7-8-18(21,10-19)11-22/h5-6,9,13,20,22H,3-4,7-8,10-11,19H2,1-2H3,(H,24,25)/t18-/m1/s1

IUPAC InChI key

ZEZFFRWWHKSMEB-GOSISDBHSA-N
IBA

wwPDB Information

Atom count

52 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2003-07-31

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



IBA : Atoms of Molecule

Total Number of Atoms: 52
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C6 C C6 N Y N 0 4.787 0.789 0.256
2 C5 C C5 N Y N 0 4.065 0.194 1.294
3 C4 C C4 N Y N 0 4.641 0.086 2.563
4 C3 C C3 N Y N 0 5.93 0.569 2.792
5 C2 C C2 N Y N 0 6.647 1.162 1.752
6 C7 C C7 N Y N 0 6.075 1.272 0.485
7 C1 C C1 N N N 0 7.99 1.666 1.99
8 O21 O O21 N N N 0 8.395 1.482 3.277
9 O20 O O20 N N N 0 8.711 2.207 1.146
10 N4 N N4 N N N 0 3.933 -0.512 3.63
11 C8 C C8 N N N 0 4.479 -0.645 4.943
12 C11 C C11 N N N 0 5.439 -1.843 4.978
13 C9 C C9 N N N 0 3.341 -0.836 5.957
14 C12 C C12 N N N 0 4.751 -3.161 4.643
15 C10 C C10 N N N 0 2.354 0.324 5.961
16 N5 N N5 N N N 0 2.744 -0.294 1.035
17 C13 C C13 R N N 0 2.411 -1.628 0.508
18 C14 C C14 N N N 0 0.93 -1.758 0.917
19 C15 C C15 N N N 0 0.389 -0.348 0.817
20 C16 C C16 N N N 0 1.58 0.498 1.189
21 O13 O O13 N N N 0 1.474 1.679 1.491
22 C18 C C18 N N N 0 2.515 -1.689 -1.027
23 O18 O O18 N N N 0 3.876 -1.558 -1.386
24 C17 C C17 N N N 0 3.167 -2.799 1.159
25 N17 N N17 N N N 0 2.619 -4.028 0.7
26 H21 H H21 N N N 0 9.3 1.82 3.447
27 H7 H H7 N N N 0 6.625 1.733 -0.332
28 H6 H H6 N N N 0 4.352 0.881 -0.736
29 H151 H 1H15 N N N 0 -0.442 -0.18 1.507
30 H152 H 2H15 N N N 0 0.084 -0.1 -0.205
31 H141 H 1H14 N N N 0 0.847 -2.096 1.959
32 H142 H 2H14 N N N 0 0.37 -2.465 0.296
33 H181 H 1H18 N N N 0 1.942 -0.874 -1.464
34 H182 H 2H18 N N N 0 2.135 -2.645 -1.382
35 H18 H H18 N N N 0 3.902 -1.245 -2.307
36 H171 H 1H17 N N N 0 3.049 -2.724 2.229
37 H172 H 2H17 N N N 0 4.206 -2.736 0.876
38 H11 H 1H1 N N N 0 1.674 -4.293 0.964
39 H12 H 2H1 N N N 0 3.224 -4.731 0.286
40 HN4 H HN4 N N N 0 3.012 -0.849 3.428
41 H8 H H8 N N N 0 5.032 0.269 5.191
42 H111 H 1H11 N N N 0 6.247 -1.685 4.253
43 H112 H 2H11 N N N 0 5.908 -1.927 5.967
44 H121 H 1H12 N N N 0 3.984 -3.412 5.382
45 H122 H 2H12 N N N 0 4.28 -3.117 3.656
46 H123 H 3H12 N N N 0 5.484 -3.974 4.632
47 H91 H 1H9 N N N 0 3.763 -0.931 6.966
48 H92 H 2H9 N N N 0 2.797 -1.766 5.75
49 H101 H 1H10 N N N 0 2.862 1.269 6.179
50 H102 H 2H10 N N N 0 1.845 0.421 4.997
51 H103 H 3H10 N N N 0 1.59 0.166 6.729
52 H3 H H3 N N N 0 6.376 0.484 3.78



IBA : Chemical Bonds

Total Number of Bonds: 53
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C6 C7 C C sing 1.39 N Y
2 C6 H6 C H sing 1.09 N N
3 C6 C5 C C doub 1.4 N Y
4 C5 N5 C N sing 1.43 N N
5 C5 C4 C C sing 1.4 N Y
6 C4 N4 C N sing 1.41 N N
7 C4 C3 C C doub 1.4 N Y
8 C3 C2 C C sing 1.4 N Y
9 C3 H3 C H sing 1.09 N N
10 C2 C1 C C sing 1.45 N N
11 C2 C7 C C doub 1.39 N Y
12 C7 H7 C H sing 1.09 N N
13 C1 O21 C O sing 1.36 N N
14 C1 O20 C O doub 1.23 N N
15 O21 H21 O H sing 0.98 N N
16 N4 HN4 N H sing 1.0 N N
17 N4 C8 N C sing 1.43 N N
18 C8 H8 C H sing 1.1 N N
19 C8 C11 C C sing 1.54 N N
20 C8 C9 C C sing 1.54 N N
21 C11 H111 C H sing 1.1 N N
22 C11 H112 C H sing 1.1 N N
23 C11 C12 C C sing 1.52 N N
24 C9 H91 C H sing 1.1 N N
25 C9 H92 C H sing 1.1 N N
26 C9 C10 C C sing 1.52 N N
27 C12 H121 C H sing 1.09 N N
28 C12 H122 C H sing 1.09 N N
29 C12 H123 C H sing 1.09 N N
30 C10 H101 C H sing 1.09 N N
31 C10 H102 C H sing 1.09 N N
32 C10 H103 C H sing 1.09 N N
33 N5 C16 N C sing 1.42 N N
34 N5 C13 N C sing 1.47 N N
35 C13 C14 C C sing 1.54 N N
36 C13 C18 C C sing 1.54 N N
37 C13 C17 C C sing 1.54 N N
38 C14 C15 C C sing 1.51 N N
39 C14 H141 C H sing 1.1 N N
40 C14 H142 C H sing 1.1 N N
41 C15 C16 C C sing 1.51 N N
42 C15 H151 C H sing 1.09 N N
43 C15 H152 C H sing 1.09 N N
44 C16 O13 C O doub 1.22 N N
45 C18 H181 C H sing 1.09 N N
46 C18 H182 C H sing 1.09 N N
47 C18 O18 C O sing 1.41 N N
48 O18 H18 O H sing 0.97 N N
49 C17 H171 C H sing 1.08 N N
50 C17 H172 C H sing 1.08 N N
51 C17 N17 C N sing 1.42 N N
52 N17 H11 N H sing 1.02 N N
53 N17 H12 N H sing 1.02 N N



IBA : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
IBA 1vcj Open in New Window Bound ligand 1 1