Chemical Components in the PDB

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9B3 : Summary

Code

9B3

One-letter code

X

Molecule name

(2~{S})-2-[(6-azanyl-5-chloranyl-pyridin-3-yl)methyl]-3-selanyl-propanoic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 (2~{S})-2-[(6-azanyl-5-chloranyl-pyridin-3-yl)methyl]-3-selanyl-propanoic acid

Formula

C9 H11 Cl N2 O2 Se

Formal charge

0

Molecular weight

293.609 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Nc1ncc(C[CH](C[SeH])C(O)=O)cc1Cl
SMILES OpenEye OEToolkits 2.0.6 c1c(cnc(c1Cl)N)CC(C[SeH])C(=O)O
Canonical SMILES CACTVS 3.385 Nc1ncc(C[C@H](C[SeH])C(O)=O)cc1Cl
Canonical SMILES OpenEye OEToolkits 2.0.6 c1c(cnc(c1Cl)N)C[C@H](C[SeH])C(=O)O

IUPAC InChI

InChI=1S/C9H11ClN2O2Se/c10-7-2-5(3-12-8(7)11)1-6(4-15)9(13)14/h2-3,6,15H,1,4H2,(H2,11,12)(H,13,14)/t6-/m1/s1

IUPAC InChI key

ZMJHVPIYUURBAQ-ZCFIWIBFSA-N
9B3

wwPDB Information

Atom count

26 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-03-01

Last modified at

2018-06-15

Status

Released

Obsoleted

Not Assigned



9B3 : Atoms of Molecule

Total Number of Atoms: 26
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 2.006 -0.259 0.745
2 C2 C C2 N Y N 0 3.241 -0.206 0.122
3 CL1 CL CL1 N N N 0 4.284 -1.594 0.114
4 C3 C C3 N Y N 0 3.636 0.976 -0.498
5 N1 N N1 N N N 0 4.874 1.044 -1.128
6 N2 N N2 N Y N 0 2.842 2.036 -0.494
7 C4 C C4 N Y N 0 1.66 2.014 0.092
8 C5 C C5 N Y N 0 1.203 0.873 0.722
9 C6 C C6 N N N 0 -0.149 0.861 1.386
10 C7 C C7 S N N 0 -1.21 0.417 0.377
11 C8 C C8 N N N 0 -0.951 -1.012 -0.028
12 O1 O O1 N N N 0 -1.761 -1.616 -0.911
13 O2 O O2 N N N 0 -0.015 -1.613 0.443
14 C9 C C9 N N N 0 -2.597 0.524 1.014
15 SE1 SE SE1 N N N 0 -3.965 0.109 -0.326
16 H1 H H1 N N N 0 1.673 -1.163 1.234
17 H2 H H2 N N N 0 5.458 0.27 -1.134
18 H3 H H3 N N N 0 5.153 1.866 -1.562
19 H4 H H4 N N N 0 1.041 2.898 0.076
20 H5 H H5 N N N 0 -0.135 0.167 2.227
21 H6 H H6 N N N 0 -0.386 1.862 1.746
22 H7 H H7 N N N 0 -1.164 1.058 -0.504
23 H8 H H8 N N N 0 -1.555 -2.533 -1.14
24 H9 H H9 N N N 0 -2.672 -0.183 1.841
25 H10 H H10 N N N 0 -2.748 1.537 1.387
26 H11 H H11 N N N 0 -5.267 0.274 0.517



9B3 : Chemical Bonds

Total Number of Bonds: 26
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N2 C4 N C doub 1.32 N Y
2 N2 C3 N C sing 1.32 N Y
3 C4 C5 C C sing 1.38 N Y
4 N1 C3 N C sing 1.39 N N
5 C3 C2 C C doub 1.39 N Y
6 C5 C6 C C sing 1.51 N N
7 C5 C1 C C doub 1.39 N Y
8 C6 C7 C C sing 1.53 N N
9 C2 C1 C C sing 1.38 N Y
10 C2 CL1 C CL sing 1.74 N N
11 C7 C9 C C sing 1.53 N N
12 C7 C8 C C sing 1.51 N N
13 C9 SE1 C SE sing 1.96 N N
14 C8 O2 C O doub 1.21 N N
15 C8 O1 C O sing 1.34 N N
16 C1 H1 C H sing 1.08 N N
17 N1 H2 N H sing 0.97 N N
18 N1 H3 N H sing 0.97 N N
19 C4 H4 C H sing 1.08 N N
20 C6 H5 C H sing 1.09 N N
21 C6 H6 C H sing 1.09 N N
22 C7 H7 C H sing 1.09 N N
23 O1 H8 O H sing 0.97 N N
24 C9 H9 C H sing 1.09 N N
25 C9 H10 C H sing 1.09 N N
26 SE1 H11 SE H sing 1.56 N N



9B3 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
9B3 5zeq Open in New Window Bound ligand 1 1