Chemical Components in the PDB

pdbe.org/chem
spacer

2BO : Summary

Code

2BO

One-letter code

X

Molecule name

N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-threonine

Systematic names

ProgramVersionName
ACDLabs 12.01 N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-threonine
OpenEye OEToolkits 1.7.6 (2S,3R)-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-butanoic acid

Formula

C12 H19 N2 O8 P

Formal charge

0

Molecular weight

350.262 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)C(O)C
SMILES CACTVS 3.385 C[CH](O)[CH](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O
SMILES OpenEye OEToolkits 1.7.6 Cc1c(c(c(cn1)COP(=O)(O)O)CNC(C(C)O)C(=O)O)O
Canonical SMILES CACTVS 3.385 C[C@@H](O)[C@H](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]([C@@H](C)O)C(=O)O)O

IUPAC InChI

InChI=1S/C12H19N2O8P/c1-6-11(16)9(4-14-10(7(2)15)12(17)18)8(3-13-6)5-22-23(19,20)21/h3,7,10,14-16H,4-5H2,1-2H3,(H,17,18)(H2,19,20,21)/t7-,10+/m1/s1

IUPAC InChI key

IZWQBQLGLAKRMN-XCBNKYQSSA-N
2BO

wwPDB Information

Atom count

42 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-09-18

Last modified at

2013-11-01

Status

Released

Obsoleted

Not Assigned



2BO : Atoms of Molecule

Total Number of Atoms: 42
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C N N N 0 -2.055 2.68 -0.633
2 C2 C C2 N Y N 0 -0.413 -3.832 0.086
3 C2A C C2A N N N 0 -1.043 -5.192 0.24
4 C3 C C3 N Y N 0 -1.171 -2.774 -0.397
5 C4 C C4 N Y N 0 -0.576 -1.525 -0.534
6 C4A C C4A N N N 0 -1.362 -0.349 -1.054
7 C5 C C5 N Y N 0 0.757 -1.387 -0.181
8 C5A C C5A N N N 0 1.446 -0.053 -0.311
9 C6 C C6 N Y N 0 1.446 -2.487 0.293
10 CA C CA S N N 0 -2.87 1.432 -0.407
11 CB C CB R N N 0 -3.952 1.711 0.638
12 CG C CG N N N 0 -4.764 0.438 0.884
13 H1 H H1 N N N 0 -1.475 -5.281 1.237
14 H10 H H10 N N N 0 5.98 1.222 0.543
15 H11 H H11 N N N 0 3.293 1.852 2.075
16 H12 H H12 N N N 0 -1.299 0.71 0.71
17 H14 H H14 N N N 0 -3.339 1.13 -1.344
18 H15 H H15 N N N 0 -4.612 2.499 0.276
19 H16 H H16 N N N 0 -2.735 1.474 2.24
20 H17 H H17 N N N 0 -2.087 4.574 -1.202
21 H18 H H18 N N N 0 -4.094 -0.367 1.189
22 H19 H H19 N N N 0 -5.495 0.619 1.672
23 H2 H H2 N N N 0 -1.827 -5.316 -0.507
24 H20 H H20 N N N 0 -5.28 0.153 -0.032
25 H3 H H3 N N N 0 -0.284 -5.962 0.102
26 H4 H H4 N N N 0 -3.093 -2.805 -0.0020
27 H5 H H5 N N N 0 -0.692 0.333 -1.579
28 H6 H H6 N N N 0 -2.132 -0.701 -1.74
29 H7 H H7 N N N 0 1.419 0.27 -1.352
30 H8 H H8 N N N 0 0.936 0.682 0.311
31 H9 H H9 N N N 0 2.485 -2.386 0.571
32 N N N N N N 0 -1.993 0.354 0.071
33 N1 N N1 N Y N 0 0.853 -3.659 0.412
34 O O O N N N 0 -2.651 3.799 -1.073
35 O1P O O1P N N N 0 3.894 1.651 -1.245
36 O2P O O2P N N N 0 5.304 0.531 0.524
37 O3 O O3 N N N 0 -2.476 -2.957 -0.73
38 O3P O O3P N N N 0 3.352 2.172 1.164
39 O4P O O4P N N N 0 2.805 -0.176 0.115
40 OB O OB N N N 0 -3.338 2.128 1.859
41 OT O OT N N N 0 -0.867 2.672 -0.417
42 P P P N N N 0 3.84 1.057 0.11



2BO : Chemical Bonds

Total Number of Bonds: 42
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OT C O C doub 1.21 N N
2 O1P P O P doub 1.48 N N
3 C O C O sing 1.34 N N
4 C CA C C sing 1.51 N N
5 O2P P O P sing 1.61 N N
6 P O4P P O sing 1.61 N N
7 P O3P P O sing 1.61 N N
8 CA N C N sing 1.47 N N
9 CA CB C C sing 1.53 N N
10 N C4A N C sing 1.47 N N
11 O4P C5A O C sing 1.43 N N
12 C4A C4 C C sing 1.51 N N
13 O3 C3 O C sing 1.36 N N
14 CB CG C C sing 1.53 N N
15 CB OB C O sing 1.43 N N
16 C4 C3 C C doub 1.39 N Y
17 C4 C5 C C sing 1.39 N Y
18 C3 C2 C C sing 1.39 N Y
19 C5A C5 C C sing 1.51 N N
20 C5 C6 C C doub 1.38 N Y
21 C2 C2A C C sing 1.51 N N
22 C2 N1 C N doub 1.32 N Y
23 C6 N1 C N sing 1.32 N Y
24 C2A H1 C H sing 1.09 N N
25 C2A H2 C H sing 1.09 N N
26 C2A H3 C H sing 1.09 N N
27 O3 H4 O H sing 0.97 N N
28 C4A H5 C H sing 1.09 N N
29 C4A H6 C H sing 1.09 N N
30 C5A H7 C H sing 1.09 N N
31 C5A H8 C H sing 1.09 N N
32 C6 H9 C H sing 1.08 N N
33 O2P H10 O H sing 0.97 N N
34 O3P H11 O H sing 0.97 N N
35 N H12 N H sing 1.01 N N
36 CA H14 C H sing 1.09 N N
37 CB H15 C H sing 1.09 N N
38 OB H16 O H sing 0.97 N N
39 O H17 O H sing 0.97 N N
40 CG H18 C H sing 1.09 N N
41 CG H19 C H sing 1.09 N N
42 CG H20 C H sing 1.09 N N



2BO : Used in PDB Entries

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