Chemical Components in the PDB

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5TX : Summary

Code

5TX

One-letter code

X

Molecule name

((3S,5S)-1,5-dihydroxy-3-methyl-2-oxopyrrolidin-3-yl)phosphonic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.4 [(3~{S},5~{S})-3-methyl-1,5-bis(oxidanyl)-2-oxidanylidene-pyrrolidin-3-yl]phosphonic acid

Formula

C5 H10 N O6 P

Formal charge

0

Molecular weight

211.11 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C[C]1(C[CH](O)N(O)C1=O)[P](O)(O)=O
SMILES OpenEye OEToolkits 2.0.4 CC1(CC(N(C1=O)O)O)P(=O)(O)O
Canonical SMILES CACTVS 3.385 C[C@@]1(C[C@H](O)N(O)C1=O)[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.4 C[C@@]1(C[C@@H](N(C1=O)O)O)P(=O)(O)O

IUPAC InChI

InChI=1S/C5H10NO6P/c1-5(13(10,11)12)2-3(7)6(9)4(5)8/h3,7,9H,2H2,1H3,(H2,10,11,12)/t3-,5-/m0/s1

IUPAC InChI key

VVBLYPMICKYZTP-UCORVYFPSA-N
5TX

wwPDB Information

Atom count

23 (13 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-12-01

Last modified at

2016-11-18

Status

Released

Obsoleted

Not Assigned



5TX : Atoms of Molecule

Total Number of Atoms: 23
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C1 S N N 0 2.017 0.849 0.662
2 C02 C C2 N N N 0 0.565 1.377 0.671
3 C03 C C3 S N N 0 -0.118 0.437 -0.349
4 C04 C C4 N N N 0 0.734 -0.813 -0.33
5 P05 P P1 N N N 0 -1.821 0.055 0.177
6 O06 O O1 N N N 0 -1.79 -0.668 1.616
7 O07 O O2 N N N 0 -2.601 1.31 0.273
8 O08 O O3 N N N 0 -2.509 -0.923 -0.9
9 C09 C C5 N N N 0 -0.118 1.068 -1.742
10 O10 O O4 N N N 0 0.396 -1.891 -0.771
11 N12 N N1 N N N 0 1.921 -0.555 0.245
12 O13 O O5 N N N 0 2.807 1.591 -0.27
13 O11 O O6 N N N 0 2.947 -1.514 0.427
14 H1 H H1 N N N 0 2.45 0.918 1.66
15 H2 H H2 N N N 0 0.118 1.271 1.66
16 H3 H H3 N N N 0 0.525 2.413 0.335
17 H4 H H4 N N N 0 -2.664 -0.9 1.958
18 H5 H H5 N N N 0 -2.05 -1.767 -1.015
19 H6 H H6 N N N 0 0.909 1.248 -2.059
20 H7 H H7 N N N 0 -0.603 0.393 -2.447
21 H8 H H8 N N N 0 -0.66 2.013 -1.713
22 H9 H H9 N N N 0 3.729 1.304 -0.32
23 H10 H H10 N N N 0 2.724 -2.395 0.096



5TX : Chemical Bonds

Total Number of Bonds: 23
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O11 N12 O N sing 1.42 N N
2 N12 C01 N C sing 1.47 N N
3 N12 C04 N C sing 1.34 N N
4 O13 C01 O C sing 1.43 N N
5 O10 C04 O C doub 1.21 N N
6 C01 C02 C C sing 1.55 N N
7 C04 C03 C C sing 1.51 N N
8 O07 P05 O P doub 1.48 N N
9 C02 C03 C C sing 1.55 N N
10 C03 P05 C P sing 1.82 N N
11 C03 C09 C C sing 1.53 N N
12 O06 P05 O P sing 1.61 N N
13 P05 O08 P O sing 1.61 N N
14 C01 H1 C H sing 1.09 N N
15 C02 H2 C H sing 1.09 N N
16 C02 H3 C H sing 1.09 N N
17 O06 H4 O H sing 0.97 N N
18 O08 H5 O H sing 0.97 N N
19 C09 H6 C H sing 1.09 N N
20 C09 H7 C H sing 1.09 N N
21 C09 H8 C H sing 1.09 N N
22 O13 H9 O H sing 0.97 N N
23 O11 H10 O H sing 0.97 N N



5TX : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
5TX 5eu9 Open in New Window Bound ligand 8 1
5TX 5tij Open in New Window Bound ligand 2 1