Chemical Components in the PDB

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CLM : Summary

Code

CLM

One-letter code

X

Molecule name

CHLORAMPHENICOL

Systematic names

ProgramVersionName
ACDLabs 10.04 2,2-dichloro-N-[(1R,2R)-2-hydroxy-1-(hydroxymethyl)-2-(4-nitrophenyl)ethyl]acetamide
OpenEye OEToolkits 1.5.0 2,2-dichloro-N-[(1R,2R)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]ethanamide

Formula

C11 H12 Cl2 N2 O5

Formal charge

0

Molecular weight

323.129 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 ClC(Cl)C(=O)NC(C(O)c1ccc([N+]([O-])=O)cc1)CO
SMILES CACTVS 3.341 OC[CH](NC(=O)C(Cl)Cl)[CH](O)c1ccc(cc1)[N+]([O-])=O
SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1C(C(CO)NC(=O)C(Cl)Cl)O)[N+](=O)[O-]
Canonical SMILES CACTVS 3.341 OC[C@@H](NC(=O)C(Cl)Cl)[C@H](O)c1ccc(cc1)[N+]([O-])=O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1[C@H]([C@@H](CO)NC(=O)C(Cl)Cl)O)[N+](=O)[O-]

IUPAC InChI

InChI=1S/C11H12Cl2N2O5/c12-10(13)11(18)14-8(5-16)9(17)6-1-3-7(4-2-6)15(19)20/h1-4,8-10,16-17H,5H2,(H,14,18)/t8-,9-/m1/s1

IUPAC InChI key

WIIZWVCIJKGZOK-RKDXNWHRSA-N
CLM

wwPDB Information

Atom count

32 (20 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



CLM : 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 N N 0 1.624 -0.247 2.332
2 CL1 CL CL1A N N N 0 2.877 0.814 3.075
3 CL2 CL CL1B N N N 0 1.081 -1.471 3.54
4 C2 C C2 N N N 0 0.447 0.589 1.901
5 O2 O O2 N N N 0 0.458 1.788 2.08
6 N2 N N2 N N N 0 -0.617 0.0050 1.316
7 C3 C C3 R N N 0 -1.76 0.818 0.897
8 C4 C C4 N N N 0 -2.766 0.914 2.046
9 O4 O O4 N N N 0 -3.217 -0.396 2.395
10 C5 C C5 R N N 0 -2.431 0.17 -0.314
11 O5 O O5 N N N 0 -2.881 -1.14 0.034
12 C6 C C6 N Y N 0 -1.44 0.076 -1.446
13 C7 C C7 N Y N 0 -0.645 -1.051 -1.572
14 C8 C C8 N Y N 0 0.263 -1.147 -2.602
15 C9 C C9 N Y N 0 0.382 -0.096 -3.527
16 N9 N N9 N N N 1 1.267 -0.18 -4.537
17 O9A O O9A N N N -1 1.366 0.732 -5.336
18 O9B O O9B N N N 0 1.968 -1.169 -4.651
19 C10 C C10 N Y N 0 -0.429 1.042 -3.39
20 C11 C C11 N Y N 0 -1.335 1.115 -2.356
21 H1 H H1 N N N 0 2.046 -0.755 1.465
22 HN2 H HN2 N N N 0 -0.625 -0.954 1.173
23 H3 H H3 N N N 0 -1.417 1.818 0.631
24 H41 H 1H4 N N N 0 -3.618 1.519 1.734
25 H42 H 2H4 N N N 0 -2.289 1.376 2.91
26 HO4 H HO4 N N N 0 -3.847 -0.291 3.121
27 H5 H H5 N N N 0 -3.282 0.775 -0.626
28 HO5 H HO5 N N N 0 -2.099 -1.642 0.303
29 H7 H H7 N N N 0 -0.737 -1.857 -0.859
30 H8 H H8 N N N 0 0.882 -2.027 -2.698
31 H10 H H10 N N N 0 -0.345 1.855 -4.096
32 H11 H H11 N N N 0 -1.959 1.99 -2.249



CLM : Chemical Bonds

Total Number of Bonds: 32
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 CL1 C CL sing 1.8 N N
2 C1 CL2 C CL sing 1.8 N N
3 C1 C2 C C sing 1.51 N N
4 C1 H1 C H sing 1.09 N N
5 C2 O2 C O doub 1.21 N N
6 C2 N2 C N sing 1.35 N N
7 N2 C3 N C sing 1.46 N N
8 N2 HN2 N H sing 0.97 N N
9 C3 C4 C C sing 1.53 N N
10 C3 C5 C C sing 1.53 N N
11 C3 H3 C H sing 1.09 N N
12 C4 O4 C O sing 1.43 N N
13 C4 H41 C H sing 1.09 N N
14 C4 H42 C H sing 1.09 N N
15 O4 HO4 O H sing 0.97 N N
16 C5 O5 C O sing 1.43 N N
17 C5 C6 C C sing 1.51 N N
18 C5 H5 C H sing 1.09 N N
19 O5 HO5 O H sing 0.97 N N
20 C6 C7 C C doub 1.38 N Y
21 C6 C11 C C sing 1.39 N Y
22 C7 C8 C C sing 1.38 N Y
23 C7 H7 C H sing 1.08 N N
24 C8 C9 C C doub 1.41 N Y
25 C8 H8 C H sing 1.08 N N
26 C9 N9 C N sing 1.35 N N
27 C9 C10 C C sing 1.4 N Y
28 N9 O9A N O sing 1.22 N N
29 N9 O9B N O doub 1.22 N N
30 C10 C11 C C doub 1.38 N Y
31 C10 H10 C H sing 1.08 N N
32 C11 H11 C H sing 1.08 N N



CLM : Used in PDB Entries

Total Number of PDB Entries: 26
Ligand Code PDB Entry ID Type Total Distinct
CLM 1cla Open in New Window Bound ligand 1 1
CLM 1k01 Open in New Window Bound ligand 1 1
CLM 1nji Open in New Window Bound ligand 1 1
CLM 1qhs Open in New Window Bound ligand 2 1
CLM 1qhy Open in New Window Bound ligand 2 1
CLM 1usq Open in New Window Bound ligand 6 1
CLM 2jkj Open in New Window Bound ligand 6 1
CLM 2jkl Open in New Window Bound ligand 6 1
CLM 2uxp Open in New Window Bound ligand 2 1
CLM 2xat Open in New Window Bound ligand 1 1
CLM 3cla Open in New Window Bound ligand 1 1
CLM 3jbv Open in New Window Bound ligand 1 1
CLM 3u9f Open in New Window Bound ligand 18 1
CLM 4bn6 Open in New Window Bound ligand 1 1
CLM 4cla Open in New Window Bound ligand 1 1
CLM 4oad Open in New Window Bound ligand 2 1
CLM 4oae Open in New Window Bound ligand 2 1
CLM 4v7t Open in New Window Bound ligand 1 1
CLM 4v7w Open in New Window Bound ligand 2 1
CLM 4zow Open in New Window Bound ligand 1 1
CLM 6iey Open in New Window Bound ligand 1 1
CLM 6nd5 Open in New Window Bound ligand 2 1
CLM 6vrz Open in New Window Bound ligand 1 1
CLM 6vs0 Open in New Window Bound ligand 1 1
CLM 6x7q Open in New Window Bound ligand 3 1
CLM 7c4g Open in New Window Bound ligand 1 1