Chemical Components in the PDB

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XPN : Summary

Code

XPN

One-letter code

X

Molecule name

Baeocystin

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 [3-[2-(methylamino)ethyl]-1~{H}-indol-4-yl] dihydrogen phosphate

Formula

C11 H15 N2 O4 P

Formal charge

0

Molecular weight

270.222 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CNCCc1c[nH]c2cccc(O[P](O)(O)=O)c12
SMILES OpenEye OEToolkits 2.0.7 CNCCc1c[nH]c2c1c(ccc2)OP(=O)(O)O
Canonical SMILES CACTVS 3.385 CNCCc1c[nH]c2cccc(O[P](O)(O)=O)c12
Canonical SMILES OpenEye OEToolkits 2.0.7 CNCCc1c[nH]c2c1c(ccc2)OP(=O)(O)O

IUPAC InChI

InChI=1S/C11H15N2O4P/c1-12-6-5-8-7-13-9-3-2-4-10(11(8)9)17-18(14,15)16/h2-4,7,12-13H,5-6H2,1H3,(H2,14,15,16)

IUPAC InChI key

WTPBXXCVZZZXKR-UHFFFAOYSA-N
XPN

wwPDB Information

Atom count

33 (18 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-06-08

Last modified at

2024-03-29

Status

Released

Obsoleted

Not Assigned



XPN : Atoms of Molecule

Total Number of Atoms: 33
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O1 O O1 N N N 0 -0.166 1.782 -1.815
2 C3 C C1 N Y N 0 0.303 -1.731 -0.679
3 C4 C C2 N Y N 0 -0.986 0.146 0.652
4 C5 C C3 N Y N 0 -2.203 0.453 1.23
5 C6 C C4 N Y N 0 -3.25 -0.456 1.184
6 C7 C C5 N Y N 0 -3.096 -1.676 0.562
7 C8 C C6 N Y N 0 -1.88 -2.008 -0.027
8 C9 C C7 N Y N 0 -0.816 -1.091 0.018
9 N N N1 N N N 0 3.823 -0.7 0.195
10 CA C C8 N N N 0 2.524 -1.367 0.36
11 CB C C9 N N N 0 1.676 -1.149 -0.895
12 C2 C C10 N Y N 0 -0.126 -2.937 -1.084
13 CM C C11 N N N 0 4.666 -0.888 1.383
14 N1 N N2 N Y N 0 -1.431 -3.118 -0.708
15 O2 O O2 N N N 0 1.082 3.32 -0.085
16 O3 O O3 N N N 0 -1.418 2.984 0.018
17 O4 O O4 N N N 0 0.038 1.038 0.699
18 P P P1 N N N 0 -0.144 2.296 -0.289
19 H3 H H1 N N N 0 0.64 1.321 -2.086
20 H5 H H2 N N N 0 -2.339 1.406 1.721
21 H6 H H3 N N N 0 -4.196 -0.204 1.64
22 H7 H H4 N N N 0 -3.919 -2.374 0.533
23 HN H H5 N N N 0 3.702 0.28 -0.012
24 HA1 H H7 N N N 0 2.681 -2.435 0.512
25 HA2 H H8 N N N 0 2.009 -0.949 1.224
26 HB1 H H9 N N N 0 2.15 -1.642 -1.743
27 HB2 H H10 N N N 0 1.591 -0.081 -1.095
28 H2 H H11 N N N 0 0.468 -3.657 -1.626
29 HM2 H H12 N N N 0 4.165 -0.466 2.254
30 HM1 H H13 N N N 0 4.838 -1.952 1.542
31 HM3 H H14 N N N 0 5.621 -0.384 1.234
32 H1 H H15 N N N 0 -1.957 -3.912 -0.888
33 H8 H H16 N N N 0 1.038 4.104 -0.65



XPN : Chemical Bonds

Total Number of Bonds: 34
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3 P O P doub 1.48 N N
2 O1 P O P sing 1.61 N N
3 P O2 P O sing 1.61 N N
4 P O4 P O sing 1.61 N N
5 C6 C5 C C doub 1.39 N Y
6 C6 C7 C C sing 1.38 N Y
7 C5 C4 C C sing 1.38 N Y
8 C7 C8 C C doub 1.39 N Y
9 C4 O4 C O sing 1.36 N N
10 C4 C9 C C doub 1.4 N Y
11 C8 C9 C C sing 1.41 N Y
12 C8 N1 C N sing 1.38 N Y
13 C9 C3 C C sing 1.47 N Y
14 N1 C2 N C sing 1.37 N Y
15 C3 C2 C C doub 1.34 N Y
16 C3 CB C C sing 1.51 N N
17 CB CA C C sing 1.53 N N
18 CM N C N sing 1.47 N N
19 CA N C N sing 1.47 N N
20 O1 H3 O H sing 0.97 N N
21 C5 H5 C H sing 1.08 N N
22 C6 H6 C H sing 1.08 N N
23 C7 H7 C H sing 1.08 N N
24 N HN N H sing 1.01 N N
25 CA HA1 C H sing 1.09 N N
26 CA HA2 C H sing 1.09 N N
27 CB HB1 C H sing 1.09 N N
28 CB HB2 C H sing 1.09 N N
29 C2 H2 C H sing 1.08 N N
30 CM HM2 C H sing 1.09 N N
31 CM HM1 C H sing 1.09 N N
32 CM HM3 C H sing 1.09 N N
33 N1 H1 N H sing 0.97 N N
34 O2 H8 O H sing 0.97 N N



XPN : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
XPN 8pb6 Open in New Window Bound ligand 1 1
XPN 8pb7 Open in New Window Bound ligand 1 1