Chemical Components in the PDB

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SNR : Summary

Code

SNR

One-letter code

X

Molecule name

NORBIOTIN

Systematic names

ProgramVersionName
ACDLabs 10.04 4-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]butanoic acid
OpenEye OEToolkits 1.5.0 4-[(3aS,4S,6aR)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]butanoic acid

Formula

C9 H14 N2 O3 S

Formal charge

0

Molecular weight

230.284 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1NC2C(SCC2N1)CCCC(=O)O
SMILES CACTVS 3.341 OC(=O)CCC[CH]1SC[CH]2NC(=O)N[CH]12
SMILES OpenEye OEToolkits 1.5.0 C1C2C(C(S1)CCCC(=O)O)NC(=O)N2
Canonical SMILES CACTVS 3.341 OC(=O)CCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12
Canonical SMILES OpenEye OEToolkits 1.5.0 C1[C@H]2[C@@H]([C@@H](S1)CCCC(=O)O)NC(=O)N2

IUPAC InChI

InChI=1S/C9H14N2O3S/c12-7(13)3-1-2-6-8-5(4-15-6)10-9(14)11-8/h5-6,8H,1-4H2,(H,12,13)(H2,10,11,14)/t5-,6-,8-/m0/s1

IUPAC InChI key

AINAXQHKYSZESH-HAFWLYHUSA-N
SNR

wwPDB Information

Atom count

29 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2002-04-10

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



SNR : Atoms of Molecule

Total Number of Atoms: 29
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -1.38 0.298 -2.867
2 N2 N N2 N N N 0 -0.234 0.419 -3.55
3 C3 C C3 R N N 0 0.765 -0.492 -2.972
4 C4 C C4 S N N 0 0.021 -1.183 -1.825
5 N5 N N5 N N N 0 -1.325 -0.591 -1.867
6 C6 C C6 S N N 0 0.644 -0.92 -0.436
7 S7 S S7 N N N 0 1.575 0.642 -0.743
8 C8 C C8 N N N 0 1.991 0.326 -2.513
9 O11 O O11 N N N 0 -2.38 0.939 -3.131
10 C12 C C12 N N N 0 -0.441 -0.714 0.621
11 C13 C C13 N N N 0 0.212 -0.377 1.963
12 C14 C C14 N N N 0 -0.872 -0.171 3.021
13 C15 C C15 N N N 0 -0.229 0.161 4.343
14 O16 O O16 N N N 0 -0.992 0.384 5.424
15 O17 O O17 N N N 0 0.974 0.226 4.429
16 HN2 H HN2 N N N 0 -0.086 1.012 -4.303
17 H3 H H3 N N N 0 1.067 -1.233 -3.713
18 H4 H H4 N N N 0 -0.035 -2.256 -2.007
19 H6 H H6 N N N 0 1.318 -1.728 -0.151
20 HN5 H HN5 N N N 0 -2.055 -0.811 -1.267
21 H81 H H81 N N N 0 2.068 1.26 -3.07
22 H82 H H82 N N N 0 2.907 -0.256 -2.602
23 H11 H 1H1 N N N 0 -1.028 -1.627 0.722
24 H21 H 1H2 N N N 0 -1.093 0.104 0.318
25 H12 H 2H1 N N N 0 0.799 0.535 1.862
26 H22 H 2H2 N N N 0 0.864 -1.196 2.266
27 H13 H 3H1 N N N 0 -1.459 -1.084 3.123
28 H23 H 3H2 N N N 0 -1.524 0.648 2.719
29 H16 H H16 N N N 0 -0.579 0.597 6.272



SNR : Chemical Bonds

Total Number of Bonds: 30
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 N2 C N sing 1.34 N N
2 C1 N5 C N sing 1.34 N N
3 C1 O11 C O doub 1.22 N N
4 N2 C3 N C sing 1.47 N N
5 N2 HN2 N H sing 0.97 N N
6 C3 C4 C C sing 1.53 N N
7 C3 C8 C C sing 1.54 N N
8 C3 H3 C H sing 1.09 N N
9 C4 N5 C N sing 1.47 N N
10 C4 C6 C C sing 1.54 N N
11 C4 H4 C H sing 1.09 N N
12 N5 HN5 N H sing 0.97 N N
13 C6 S7 C S sing 1.84 N N
14 C6 C12 C C sing 1.53 N N
15 C6 H6 C H sing 1.09 N N
16 S7 C8 S C sing 1.85 N N
17 C8 H81 C H sing 1.09 N N
18 C8 H82 C H sing 1.09 N N
19 C12 C13 C C sing 1.53 N N
20 C12 H11 C H sing 1.09 N N
21 C12 H21 C H sing 1.09 N N
22 C13 C14 C C sing 1.53 N N
23 C13 H12 C H sing 1.09 N N
24 C13 H22 C H sing 1.09 N N
25 C14 C15 C C sing 1.51 N N
26 C14 H13 C H sing 1.09 N N
27 C14 H23 C H sing 1.09 N N
28 C15 O16 C O sing 1.34 N N
29 C15 O17 C O doub 1.21 N N
30 O16 H16 O H sing 0.97 N N



SNR : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
SNR 1lcv Open in New Window Bound ligand 2 1
SNR 1ldo Open in New Window Bound ligand 2 1