Chemical Components in the PDB

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42E : Summary

Code

42E

One-letter code

X

Molecule name

[(2R,5S)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-1,3-oxathiolan-2-yl]methyl dihydrogen phosphate

Systematic names

ProgramVersionName
ACDLabs 12.01 [(2R,5S)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-1,3-oxathiolan-2-yl]methyl dihydrogen phosphate
OpenEye OEToolkits 1.7.6 [(2R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methyl dihydrogen phosphate

Formula

C8 H12 N3 O6 P S

Formal charge

0

Molecular weight

309.236 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CS2
SMILES CACTVS 3.385 NC1=NC(=O)N(C=C1)[CH]2CS[CH](CO[P](O)(O)=O)O2
SMILES OpenEye OEToolkits 1.7.6 C1C(OC(S1)COP(=O)(O)O)N2C=CC(=NC2=O)N
Canonical SMILES CACTVS 3.385 NC1=NC(=O)N(C=C1)[C@@H]2CS[C@H](CO[P](O)(O)=O)O2
Canonical SMILES OpenEye OEToolkits 1.7.6 C1[C@H](O[C@H](S1)COP(=O)(O)O)N2C=CC(=NC2=O)N

IUPAC InChI

InChI=1S/C8H12N3O6PS/c9-5-1-2-11(8(12)10-5)6-4-19-7(17-6)3-16-18(13,14)15/h1-2,6-7H,3-4H2,(H2,9,10,12)(H2,13,14,15)/t6-,7+/m0/s1

IUPAC InChI key

WUMZLKDCOINBEA-NKWVEPMBSA-N
42E

wwPDB Information

Atom count

31 (19 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-01-29

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



42E : Atoms of Molecule

Total Number of Atoms: 31
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 PA P PA N N N 0 3.118 -0.976 -0.094
2 O1A O O1A N N N 0 3.671 -1.284 1.244
3 O2A O O2A N N N 0 2.497 -2.314 -0.739
4 O5' O O5' N N N 0 1.964 0.138 0.046
5 C5' C C5' N N N 0 2.174 1.401 0.679
6 C4' C C4' R N N 0 0.879 2.214 0.639
7 O4' O O4' N N N 0 -0.18 1.521 1.325
8 S3' S S3' N N N 0 0.234 2.331 -1.082
9 C2' C C2' N N N 0 -1.52 2.47 -0.533
10 C1' C C1' S N N 0 -1.479 1.634 0.769
11 N1 N N1 N N N 0 -1.985 0.29 0.48
12 C2 C C2 N N N 0 -3.197 0.138 -0.085
13 O2 O O2 N N N 0 -3.863 1.125 -0.35
14 N3 N N3 N N N 0 -3.681 -1.072 -0.358
15 C4 C C4 N N N 0 -2.978 -2.162 -0.08
16 N4 N N4 N N N 0 -3.488 -3.407 -0.367
17 C5 C C5 N N N 0 -1.704 -2.037 0.513
18 C6 C C6 N N N 0 -1.224 -0.799 0.779
19 H2 H H2 N N N 0 3.137 -3.03 -0.853
20 H3 H H3 N N N 0 2.472 1.242 1.716
21 H4 H H4 N N N 0 2.961 1.944 0.155
22 H5 H H5 N N N 0 1.033 3.205 1.066
23 H6 H H6 N N N 0 -1.787 3.507 -0.327
24 H7 H H7 N N N 0 -2.198 2.029 -1.263
25 H8 H H8 N N N 0 -2.135 2.1 1.504
26 H9 H H9 N N N 0 -4.364 -3.489 -0.775
27 H10 H H10 N N N 0 -2.971 -4.201 -0.162
28 H11 H H11 N N N 0 -1.118 -2.914 0.742
29 H12 H H12 N N N 0 -0.251 -0.678 1.232
30 OP3 O OP3 N N Y 0 4.292 -0.417 -1.044
31 H1 H H1 N N Y 0 4.001 -0.194 -1.938



42E : 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 O1A PA O P doub 1.48 N N
2 O2A PA O P sing 1.61 N N
3 PA O5' P O sing 1.61 N N
4 O5' C5' O C sing 1.43 N N
5 C5' C4' C C sing 1.53 N N
6 S3' C4' S C sing 1.84 N N
7 S3' C2' S C sing 1.84 N N
8 C5 C6 C C doub 1.35 N N
9 C5 C4 C C sing 1.41 N N
10 C4' O4' C O sing 1.44 N N
11 C6 N1 C N sing 1.36 N N
12 N4 C4 N C sing 1.38 N N
13 C4 N3 C N doub 1.33 N N
14 C2' C1' C C sing 1.55 N N
15 O4' C1' O C sing 1.42 N N
16 N1 C1' N C sing 1.46 N N
17 N1 C2 N C sing 1.35 N N
18 N3 C2 N C sing 1.33 N N
19 C2 O2 C O doub 1.22 N N
20 O2A H2 O H sing 0.97 N N
21 C5' H3 C H sing 1.09 N N
22 C5' H4 C H sing 1.09 N N
23 C4' H5 C H sing 1.09 N N
24 C2' H6 C H sing 1.09 N N
25 C2' H7 C H sing 1.09 N N
26 C1' H8 C H sing 1.09 N N
27 N4 H9 N H sing 0.97 N N
28 N4 H10 N H sing 0.97 N N
29 C5 H11 C H sing 1.08 N N
30 C6 H12 C H sing 1.08 N N
31 PA OP3 P O sing 1.61 N N
32 OP3 H1 O H sing 0.97 N N



42E : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
42E 5tba Open in New Window Bound ligand 1 1
42E 5tbc Open in New Window Bound ligand 1 1