Chemical Components in the PDB

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PIR : Summary

Code

PIR

One-letter code

X

Molecule name

2-(4-AMINO-PHENYL)-5-HYDROXYMETHYL-PYRROLIDINE-3,4-DIOL

Systematic names

ProgramVersionName
ACDLabs 10.04 (2S,3S,4R,5R)-2-(4-aminophenyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol
OpenEye OEToolkits 1.5.0 (2S,3S,4R,5R)-2-(4-aminophenyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol

Formula

C11 H16 N2 O3

Formal charge

0

Molecular weight

224.256 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 OC2C(c1ccc(N)cc1)NC(CO)C2O
SMILES CACTVS 3.341 Nc1ccc(cc1)[CH]2N[CH](CO)[CH](O)[CH]2O
SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1C2C(C(C(N2)CO)O)O)N
Canonical SMILES CACTVS 3.341 Nc1ccc(cc1)[C@@H]2N[C@H](CO)[C@@H](O)[C@H]2O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1[C@H]2[C@@H]([C@@H]([C@H](N2)CO)O)O)N

IUPAC InChI

InChI=1S/C11H16N2O3/c12-7-3-1-6(2-4-7)9-11(16)10(15)8(5-14)13-9/h1-4,8-11,13-16H,5,12H2/t8-,9+,10-,11+/m1/s1

IUPAC InChI key

SQENVZNKXLCDLF-YTWAJWBKSA-N
PIR

wwPDB Information

Atom count

32 (16 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



PIR : Atoms of Molecule

Total Number of Atoms: 32
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 0.423 0.876 1.524
2 C2 C C2 N Y N 0 -0.097 -0.347 1.146
3 C3 C C3 N Y N 0 -0.398 -1.299 2.102
4 C4 C C4 N Y N 0 -0.181 -1.03 3.439
5 C5 C C5 N Y N 0 0.341 0.198 3.823
6 N5 N N5 N N N 0 0.562 0.474 5.174
7 C6 C C6 N Y N 0 0.638 1.154 2.86
8 C1' C C1' S N N 0 -0.335 -0.644 -0.311
9 C2' C C2' S N N 0 -1.301 0.394 -0.922
10 O2' O O2' N N N 0 -2.631 -0.124 -0.97
11 C3' C C3' R N N 0 -0.769 0.641 -2.351
12 O3' O O3' N N N 0 -1.757 0.279 -3.317
13 C4' C C4' R N N 0 0.468 -0.271 -2.482
14 N4' N N4' N N N 0 0.923 -0.489 -1.085
15 C5' C C5' N N N 0 1.562 0.422 -3.297
16 O5' O O5' N N N 0 2.724 -0.407 -3.339
17 H1 H H1 N N N 0 0.658 1.618 0.774
18 H3 H H3 N N N 0 -0.804 -2.254 1.803
19 HN51 H 1HN5 N N N 0 0.927 1.332 5.441
20 H4 H H4 N N N 0 -0.416 -1.774 4.186
21 HN52 H 2HN5 N N N 0 0.347 -0.191 5.846
22 H6 H H6 N N N 0 1.045 2.11 3.154
23 H1' H H1' N N N 0 -0.734 -1.651 -0.433
24 H2' H H2' N N N 0 -1.276 1.317 -0.343
25 HO2' H 'HO2 N N N 0 -3.177 0.547 -1.401
26 H3' H H3' N N N 0 -0.484 1.686 -2.474
27 HO3' H 'HO3 N N N 0 -2.505 0.879 -3.19
28 H4' H H4' N N N 0 0.194 -1.219 -2.945
29 HN4' H 'HN4 N N N 0 1.387 -1.384 -1.067
30 H5'1 H 1H5' N N N 0 1.203 0.598 -4.311
31 H5'2 H 2H5' N N N 0 1.813 1.375 -2.83
32 HO5' H 'HO5 N N N 0 3.387 0.065 -3.861



PIR : Chemical Bonds

Total Number of Bonds: 33
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C doub 1.38 N Y
2 C1 C6 C C sing 1.38 N Y
3 C1 H1 C H sing 1.08 N N
4 C2 C3 C C sing 1.38 N Y
5 C2 C1' C C sing 1.51 N N
6 C3 C4 C C doub 1.38 N Y
7 C3 H3 C H sing 1.08 N N
8 C4 C5 C C sing 1.39 N Y
9 C4 H4 C H sing 1.08 N N
10 C5 N5 C N sing 1.4 N N
11 C5 C6 C C doub 1.39 N Y
12 N5 HN51 N H sing 0.97 N N
13 N5 HN52 N H sing 0.97 N N
14 C6 H6 C H sing 1.08 N N
15 C1' C2' C C sing 1.54 N N
16 C1' N4' C N sing 1.49 N N
17 C1' H1' C H sing 1.09 N N
18 C2' O2' C O sing 1.43 N N
19 C2' C3' C C sing 1.54 N N
20 C2' H2' C H sing 1.09 N N
21 O2' HO2' O H sing 0.97 N N
22 C3' O3' C O sing 1.43 N N
23 C3' C4' C C sing 1.54 N N
24 C3' H3' C H sing 1.09 N N
25 O3' HO3' O H sing 0.97 N N
26 C4' N4' C N sing 1.49 N N
27 C4' C5' C C sing 1.53 N N
28 C4' H4' C H sing 1.09 N N
29 N4' HN4' N H sing 1.01 N N
30 C5' O5' C O sing 1.43 N N
31 C5' H5'1 C H sing 1.09 N N
32 C5' H5'2 C H sing 1.09 N N
33 O5' HO5' O H sing 0.97 N N



PIR : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
PIR 2mas Open in New Window Bound ligand 4 1