Chemical Components in the PDB

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N9D : Summary

Code

N9D

One-letter code

X

Molecule name

(3R,5S)-5-[(2R)-2-amino-2-carboxyethyl]-1-(4-propylphenyl)pyrazolidine-3-carboxylic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (3R,5S)-5-[(2R)-2-amino-2-carboxyethyl]-1-(4-propylphenyl)pyrazolidine-3-carboxylic acid
OpenEye OEToolkits 2.0.7 (3~{R},5~{S})-5-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]-1-(4-propylphenyl)pyrazolidine-3-carboxylic acid

Formula

C16 H23 N3 O4

Formal charge

0

Molecular weight

321.372 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c2c(ccc(N1C(CC(C(O)=O)N)CC(C(=O)O)N1)c2)CCC
SMILES CACTVS 3.385 CCCc1ccc(cc1)N2N[CH](C[CH]2C[CH](N)C(O)=O)C(O)=O
SMILES OpenEye OEToolkits 2.0.7 CCCc1ccc(cc1)N2C(CC(N2)C(=O)O)CC(C(=O)O)N
Canonical SMILES CACTVS 3.385 CCCc1ccc(cc1)N2N[C@H](C[C@@H]2C[C@@H](N)C(O)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 CCCc1ccc(cc1)N2[C@H](C[C@@H](N2)C(=O)O)C[C@H](C(=O)O)N

IUPAC InChI

InChI=1S/C16H23N3O4/c1-2-3-10-4-6-11(7-5-10)19-12(8-13(17)15(20)21)9-14(18-19)16(22)23/h4-7,12-14,18H,2-3,8-9,17H2,1H3,(H,20,21)(H,22,23)/t12-,13+,14+/m0/s1

IUPAC InChI key

UPNZKJBKYMIUDF-BFHYXJOUSA-N
N9D

wwPDB Information

Atom count

46 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-05-08

Last modified at

2020-05-08

Status

Released

Obsoleted

Not Assigned



N9D : Atoms of Molecule

Total Number of Atoms: 46
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C11 C C1 N Y N 0 -2.971 -0.318 -1.365
2 C17 C C2 N Y N 0 -2.37 -0.473 0.95
3 C18 C C3 N Y N 0 -1.07 -0.775 0.597
4 C19 C C4 N N N 0 3.516 -2.458 0.584
5 O20 O O1 N N N 0 4.595 -2.162 1.326
6 C02 C C5 R N N 0 1.738 2.405 -0.351
7 C03 C C6 N N N 0 0.867 1.151 -0.253
8 C04 C C7 S N N 0 1.427 0.068 -1.177
9 C05 C C8 N N N 0 2.82 -0.402 -0.684
10 C06 C C9 R N N 0 2.424 -1.436 0.402
11 C09 C C10 N Y N 0 -0.716 -0.85 -0.744
12 C10 C C11 N Y N 0 -1.672 -0.62 -1.725
13 C12 C C12 N Y N 0 -3.32 -0.245 -0.029
14 C13 C C13 N N N 0 -4.738 0.085 0.361
15 C14 C C14 N N N 0 -5.546 -1.208 0.484
16 C15 C C15 N N N 0 -6.986 -0.873 0.879
17 C22 C C16 N N N 0 1.252 3.433 0.637
18 N01 N N1 N N N 0 1.654 2.955 -1.711
19 N07 N N2 N N N 0 1.204 -2.07 -0.145
20 N08 N N3 N N N 0 0.598 -1.156 -1.105
21 O21 O O2 N N N 0 3.421 -3.543 0.062
22 O23 O O3 N N N 0 0.552 4.345 0.266
23 O24 O O4 N N N 0 1.596 3.336 1.931
24 H1 H H1 N N N 0 -3.713 -0.135 -2.127
25 H2 H H2 N N N 0 -2.646 -0.415 1.993
26 H3 H H3 N N N 0 -0.329 -0.953 1.362
27 H4 H H4 N N N 0 5.27 -2.849 1.414
28 H5 H H5 N N N 0 2.773 2.147 -0.127
29 H6 H H6 N N N 0 0.867 0.788 0.775
30 H7 H H7 N N N 0 -0.153 1.393 -0.553
31 H8 H H8 N N N 0 1.487 0.433 -2.202
32 H9 H H9 N N N 0 3.381 -0.876 -1.489
33 H10 H H10 N N N 0 3.382 0.425 -0.251
34 H11 H H11 N N N 0 2.208 -0.936 1.346
35 H12 H H12 N N N 0 -1.4 -0.678 -2.769
36 H13 H H13 N N N 0 -4.739 0.607 1.317
37 H14 H H14 N N N 0 -5.185 0.722 -0.402
38 H15 H H15 N N N 0 -5.545 -1.73 -0.473
39 H16 H H16 N N N 0 -5.099 -1.845 1.246
40 H17 H H17 N N N 0 -6.988 -0.351 1.836
41 H18 H H18 N N N 0 -7.433 -0.236 0.117
42 H19 H H19 N N N 0 -7.562 -1.794 0.967
43 H20 H H20 N N N 0 0.719 3.274 -1.914
44 H21 H H21 N N N 0 2.327 3.695 -1.843
45 H23 H H23 N N N 0 0.555 -2.303 0.592
46 H25 H H25 N N N 0 1.26 4.019 2.528



N9D : Chemical Bonds

Total Number of Bonds: 47
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C13 C12 C C sing 1.51 N N
2 C13 C14 C C sing 1.53 N N
3 C11 C12 C C doub 1.38 N Y
4 C11 C10 C C sing 1.38 N Y
5 C12 C17 C C sing 1.38 N Y
6 C14 C15 C C sing 1.53 N N
7 C10 C09 C C doub 1.39 N Y
8 C17 C18 C C doub 1.38 N Y
9 C09 C18 C C sing 1.39 N Y
10 C09 N08 C N sing 1.4 N N
11 N08 C04 N C sing 1.48 N N
12 N08 N07 N N sing 1.46 N N
13 N01 C02 N C sing 1.47 N N
14 C04 C03 C C sing 1.53 N N
15 C04 C05 C C sing 1.55 N N
16 C03 C02 C C sing 1.53 N N
17 N07 C06 N C sing 1.48 N N
18 C02 C22 C C sing 1.51 N N
19 O23 C22 O C doub 1.21 N N
20 C05 C06 C C sing 1.55 N N
21 C22 O24 C O sing 1.34 N N
22 C06 C19 C C sing 1.51 N N
23 C19 O21 C O doub 1.21 N N
24 C19 O20 C O sing 1.34 N N
25 C11 H1 C H sing 1.08 N N
26 C17 H2 C H sing 1.08 N N
27 C18 H3 C H sing 1.08 N N
28 O20 H4 O H sing 0.97 N N
29 C02 H5 C H sing 1.09 N N
30 C03 H6 C H sing 1.09 N N
31 C03 H7 C H sing 1.09 N N
32 C04 H8 C H sing 1.09 N N
33 C05 H9 C H sing 1.09 N N
34 C05 H10 C H sing 1.09 N N
35 C06 H11 C H sing 1.09 N N
36 C10 H12 C H sing 1.08 N N
37 C13 H13 C H sing 1.09 N N
38 C13 H14 C H sing 1.09 N N
39 C14 H15 C H sing 1.09 N N
40 C14 H16 C H sing 1.09 N N
41 C15 H17 C H sing 1.09 N N
42 C15 H18 C H sing 1.09 N N
43 C15 H19 C H sing 1.09 N N
44 N01 H20 N H sing 1.01 N N
45 N01 H21 N H sing 1.01 N N
46 N07 H23 N H sing 1.01 N N
47 O24 H25 O H sing 0.97 N N



N9D : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
N9D 6ove Open in New Window Bound ligand 1 1