Chemical Components in the PDB

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LCS : Summary

Code

LCS

One-letter code

X

Molecule name

[5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate

Systematic names

ProgramVersionName
ACDLabs 12.01 [5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate
OpenEye OEToolkits 1.7.2 [6-methyl-5-oxidanyl-4-[[(E)-(3-oxidanylidene-1,2-oxazolidin-4-ylidene)amino]methyl]pyridin-3-yl]methyl dihydrogen phosphate

Formula

C11 H14 N3 O7 P

Formal charge

0

Molecular weight

331.219 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C2/C(=N/Cc1c(cnc(c1O)C)COP(=O)(O)O)CON2
SMILES CACTVS 3.370 Cc1ncc(CO[P](O)(O)=O)c(CN=C2CONC2=O)c1O
SMILES OpenEye OEToolkits 1.7.2 Cc1c(c(c(cn1)COP(=O)(O)O)CN=C2CONC2=O)O
Canonical SMILES CACTVS 3.370 Cc1ncc(CO[P](O)(O)=O)c(CN=C2CONC2=O)c1O
Canonical SMILES OpenEye OEToolkits 1.7.2 Cc1c(c(c(cn1)COP(=O)(O)O)C/N=C/2\CONC2=O)O

IUPAC InChI

InChI=1S/C11H14N3O7P/c1-6-10(15)8(3-13-9-5-20-14-11(9)16)7(2-12-6)4-21-22(17,18)19/h2,15H,3-5H2,1H3,(H,14,16)(H2,17,18,19)/b13-9+

IUPAC InChI key

KFCQHWOGBVCKHR-UKTHLTGXSA-N
LCS

wwPDB Information

Atom count

36 (22 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-11-17

Last modified at

2011-07-21

Status

Released

Obsoleted

Not Assigned



LCS : Atoms of Molecule

Total Number of Atoms: 36
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 0.646 -3.239 -0.785
2 C2 C C2 N Y N 0 -0.625 -3.318 -0.445
3 C2A C C2A N N N 0 -1.412 -4.557 -0.784
4 C3 C C3 N Y N 0 -1.245 -2.272 0.223
5 O3 O O3 N N N 0 -2.556 -2.358 0.573
6 C4 C C4 N Y N 0 -0.507 -1.134 0.53
7 C4A C C4A N N N 0 -1.141 0.026 1.255
8 C5 C C5 N Y N 0 0.826 -1.092 0.153
9 C6 C C6 N Y N 0 1.374 -2.174 -0.51
10 C5A C C5A N N N 0 1.668 0.119 0.462
11 O4P O O4P N N N 0 2.959 -0.034 -0.132
12 P P P N N N 0 4.12 1.074 -0.005
13 ND N ND N N N 0 -4.778 2.316 -0.511
14 O1P O O1P N N N 0 3.61 2.379 -0.481
15 O2P O O2P N N N 0 4.572 1.202 1.535
16 O3P O O3P N N N 0 5.383 0.632 -0.9
17 N N N N N N 0 -1.583 1.027 0.281
18 CA C CA N N N 0 -2.828 1.306 0.17
19 C C C N N N 0 -3.447 2.353 -0.685
20 O O O N N N 0 -2.849 3.115 -1.418
21 HO3 H HO3 N N N 0 -2.705 -2.741 1.449
22 OG O OG N N N 0 -5.158 1.316 0.408
23 CB C CB N N N 0 -3.988 0.635 0.874
24 H2A1 H H2A1 N N N 0 -1.335 -5.272 0.035
25 H2A2 H H2A2 N N N 0 -2.458 -4.293 -0.937
26 H2A3 H H2A3 N N N 0 -1.013 -5.003 -1.695
27 H4A1 H H4A1 N N N 0 -1.998 -0.329 1.827
28 H4A2 H H4A2 N N N 0 -0.412 0.473 1.931
29 H6 H H6 N N N 0 2.412 -2.148 -0.805
30 H5A1 H H5A1 N N N 0 1.186 1.009 0.058
31 H5A2 H H5A2 N N N 0 1.775 0.221 1.542
32 HOP2 H HOP2 N N N 0 4.918 0.382 1.913
33 HOP3 H HOP3 N N N 0 6.122 1.255 -0.871
34 HND H HND N N N 0 -5.402 2.905 -0.962
35 HB1 H HB1 N N N 0 -4.032 -0.422 0.608
36 HB2 H HB2 N N N 0 -3.892 0.749 1.954



LCS : Chemical Bonds

Total Number of Bonds: 37
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C doub 1.32 N Y
2 N1 C6 N C sing 1.32 N Y
3 C2 C2A C C sing 1.51 N N
4 C2 C3 C C sing 1.39 N Y
5 C3 O3 C O sing 1.36 N N
6 C3 C4 C C doub 1.39 N Y
7 C4 C4A C C sing 1.51 N N
8 C4 C5 C C sing 1.39 N Y
9 C4A N C N sing 1.46 N N
10 C5 C6 C C doub 1.38 N Y
11 C5 C5A C C sing 1.51 N N
12 C5A O4P C O sing 1.43 N N
13 O4P P O P sing 1.61 N N
14 P O1P P O doub 1.48 N N
15 P O2P P O sing 1.61 N N
16 P O3P P O sing 1.61 N N
17 N CA N C doub 1.28 N N
18 CA C C C sing 1.49 N N
19 CA CB C C sing 1.51 N N
20 C O C O doub 1.21 N N
21 C ND C N sing 1.34 N N
22 ND OG N O sing 1.41 N N
23 OG CB O C sing 1.43 N N
24 C2A H2A1 C H sing 1.09 N N
25 C2A H2A2 C H sing 1.09 N N
26 C2A H2A3 C H sing 1.09 N N
27 O3 HO3 O H sing 0.97 N N
28 C4A H4A1 C H sing 1.09 N N
29 C4A H4A2 C H sing 1.09 N N
30 C6 H6 C H sing 1.08 N N
31 C5A H5A1 C H sing 1.09 N N
32 C5A H5A2 C H sing 1.09 N N
33 O2P HOP2 O H sing 0.97 N N
34 O3P HOP3 O H sing 0.97 N N
35 ND HND N H sing 0.97 N N
36 CB HB1 C H sing 1.09 N N
37 CB HB2 C H sing 1.09 N N



LCS : Used in PDB Entries

Total Number of PDB Entries: 6
Ligand Code PDB Entry ID Type Total Distinct
LCS 1d7u Open in New Window Bound ligand 1 1
LCS 4d9e Open in New Window Bound ligand 4 1
LCS 4oma Open in New Window Bound ligand 1 1
LCS 6qp1 Open in New Window Bound ligand 2 1
LCS 8ahu Open in New Window Bound ligand 1 1
LCS 8aie Open in New Window Bound ligand 1 1