Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

379 : Summary

Code

379

One-letter code

X

Molecule name

3-{[(R)-1-amino-3-(pyridin-3-yl)propyl](hydroxy)phosphoryl}-(S)-2-benzylpropanoic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S)-3-[(S)-[(1R)-1-amino-3-(pyridin-3-yl)propyl](hydroxy)phosphoryl]-2-benzylpropanoic acid
OpenEye OEToolkits 1.7.6 (2S)-2-[[[(1R)-1-azanyl-3-pyridin-3-yl-propyl]-oxidanyl-phosphoryl]methyl]-3-phenyl-propanoic acid

Formula

C18 H23 N2 O4 P

Formal charge

0

Molecular weight

362.36 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C(Cc1ccccc1)CP(=O)(O)C(N)CCc2cccnc2
SMILES CACTVS 3.385 N[CH](CCc1cccnc1)[P](O)(=O)C[CH](Cc2ccccc2)C(O)=O
SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)CC(CP(=O)(C(CCc2cccnc2)N)O)C(=O)O
Canonical SMILES CACTVS 3.385 N[C@@H](CCc1cccnc1)[P](O)(=O)C[C@@H](Cc2ccccc2)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)C[C@H](CP(=O)([C@H](CCc2cccnc2)N)O)C(=O)O

IUPAC InChI

InChI=1S/C18H23N2O4P/c19-17(9-8-15-7-4-10-20-12-15)25(23,24)13-16(18(21)22)11-14-5-2-1-3-6-14/h1-7,10,12,16-17H,8-9,11,13,19H2,(H,21,22)(H,23,24)/t16-,17-/m1/s1

IUPAC InChI key

LWRKOPLMYMXZKW-IAGOWNOFSA-N
379

wwPDB Information

Atom count

48 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-06-27

Last modified at

2014-09-19

Status

Released

Obsoleted

Not Assigned



379 : Atoms of Molecule

Total Number of Atoms: 48
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P11 P P11 N N N 0 -0.472 0.84 -0.094
2 C1 C C1 N N N 0 -3.161 1.38 -0.061
3 C3 C C3 R N N 0 -1.822 1.968 0.387
4 C6 C C6 N N N 0 -3.371 0.02 0.608
5 C8 C C8 N Y N 0 -4.69 -0.559 0.167
6 N10 N N10 N N N 0 -1.621 3.274 -0.256
7 C11 C C11 N N N 0 1.124 1.541 0.44
8 O12 O O12 N N N 0 -0.47 0.657 -1.693
9 C13 C C13 S N N 0 2.243 0.539 0.149
10 O13 O O13 N N N 0 -0.675 -0.475 0.554
11 C15 C C15 N N N 0 2.191 -0.578 1.159
12 C16 C C16 N N N 0 3.597 1.247 0.241
13 C01 C C01 N Y N 0 -4.761 -1.362 -0.956
14 C17 C C17 N Y N 0 4.69 0.292 -0.165
15 N18 N N18 N Y N 0 -5.913 -1.873 -1.348
16 C19 C C19 N Y N 0 -7.033 -1.641 -0.692
17 C20 C C20 N Y N 0 -7.039 -0.847 0.439
18 C21 C C21 N Y N 0 -5.847 -0.297 0.885
19 O23 O O23 N N N 0 1.346 -0.574 2.022
20 O24 O O24 N N N 0 3.085 -1.579 1.099
21 C36 C C36 N Y N 0 5.082 0.212 -1.488
22 C37 C C37 N Y N 0 6.085 -0.663 -1.86
23 C38 C C38 N Y N 0 6.697 -1.458 -0.909
24 C39 C C39 N Y N 0 6.306 -1.377 0.414
25 C40 C C40 N Y N 0 5.306 -0.498 0.787
26 H1 H H1 N N N 0 -3.968 2.054 0.226
27 H2 H H2 N N N 0 -3.16 1.256 -1.144
28 H12 H H12 N N N 0 -1.824 2.092 1.469
29 H6 H H6 N N N 0 -2.564 -0.654 0.321
30 H7 H H7 N N N 0 -3.372 0.145 1.691
31 H11 H H11 N N N 0 -1.615 3.185 -1.261
32 H13 H H13 N N N 0 -2.32 3.936 0.045
33 H16 H H16 N N N 0 1.314 2.467 -0.103
34 H17 H H17 N N N 0 1.09 1.748 1.51
35 H4 H H4 N N N 0 -0.342 1.48 -2.183
36 H18 H H18 N N N 0 2.114 0.13 -0.853
37 H19 H H19 N N N 0 3.602 2.109 -0.426
38 H20 H H20 N N N 0 3.765 1.578 1.265
39 H8 H H8 N N N 0 -3.864 -1.574 -1.518
40 H10 H H10 N N N 0 -7.957 -2.076 -1.044
41 H14 H H14 N N N 0 -7.96 -0.661 0.971
42 H15 H H15 N N N 0 -5.821 0.324 1.768
43 H9 H H9 N N N 0 3.012 -2.273 1.768
44 H21 H H21 N N N 0 4.604 0.833 -2.232
45 H22 H H22 N N N 0 6.39 -0.727 -2.894
46 H25 H H25 N N N 0 7.48 -2.142 -1.2
47 H23 H H23 N N N 0 6.784 -1.998 1.158
48 H24 H H24 N N N 0 5.003 -0.432 1.822



379 : Chemical Bonds

Total Number of Bonds: 49
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P11 C3 P C sing 1.82 N N
2 P11 C11 P C sing 1.82 N N
3 P11 O12 P O sing 1.61 N N
4 P11 O13 P O doub 1.48 N N
5 C1 C3 C C sing 1.53 N N
6 C1 C6 C C sing 1.53 N N
7 C3 N10 C N sing 1.47 N N
8 C6 C8 C C sing 1.51 N N
9 C8 C01 C C doub 1.38 N Y
10 C8 C21 C C sing 1.39 N Y
11 C11 C13 C C sing 1.53 N N
12 C13 C15 C C sing 1.51 N N
13 C13 C16 C C sing 1.53 N N
14 C15 O23 C O doub 1.21 N N
15 C15 O24 C O sing 1.34 N N
16 C16 C17 C C sing 1.51 N N
17 C01 N18 C N sing 1.32 N Y
18 C17 C36 C C doub 1.38 N Y
19 C17 C40 C C sing 1.38 N Y
20 N18 C19 N C doub 1.32 N Y
21 C19 C20 C C sing 1.38 N Y
22 C20 C21 C C doub 1.39 N Y
23 C36 C37 C C sing 1.38 N Y
24 C37 C38 C C doub 1.38 N Y
25 C38 C39 C C sing 1.38 N Y
26 C39 C40 C C doub 1.38 N Y
27 C1 H1 C H sing 1.09 N N
28 C1 H2 C H sing 1.09 N N
29 C3 H12 C H sing 1.09 N N
30 C6 H6 C H sing 1.09 N N
31 C6 H7 C H sing 1.09 N N
32 N10 H11 N H sing 1.01 N N
33 N10 H13 N H sing 1.01 N N
34 C11 H16 C H sing 1.09 N N
35 C11 H17 C H sing 1.09 N N
36 O12 H4 O H sing 0.97 N N
37 C13 H18 C H sing 1.09 N N
38 C16 H19 C H sing 1.09 N N
39 C16 H20 C H sing 1.09 N N
40 C01 H8 C H sing 1.08 N N
41 C19 H10 C H sing 1.08 N N
42 C20 H14 C H sing 1.08 N N
43 C21 H15 C H sing 1.08 N N
44 O24 H9 O H sing 0.97 N N
45 C36 H21 C H sing 1.08 N N
46 C37 H22 C H sing 1.08 N N
47 C38 H25 C H sing 1.08 N N
48 C39 H23 C H sing 1.08 N N
49 C40 H24 C H sing 1.08 N N



379 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
379 4qir Open in New Window Bound ligand 1 1