Chemical Components in the PDB

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G5Q : Summary

Code

G5Q

One-letter code

X

Molecule name

5'-O-(N-(L-aspartyl)-sulfamoyl)N3-methyluridine

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 (3~{S})-3-azanyl-4-[[(2~{R},3~{S},4~{R},5~{R})-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxysulfonylamino]-4-oxidanylidene-butanoic acid

Formula

C14 H20 N4 O11 S

Formal charge

0

Molecular weight

452.394 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN1C(=O)C=CN([CH]2O[CH](CO[S](=O)(=O)NC(=O)[CH](N)CC(O)=O)[CH](O)[CH]2O)C1=O
SMILES OpenEye OEToolkits 2.0.6 CN1C(=O)C=CN(C1=O)C2C(C(C(O2)COS(=O)(=O)NC(=O)C(CC(=O)O)N)O)O
Canonical SMILES CACTVS 3.385 CN1C(=O)C=CN([C@@H]2O[C@H](CO[S](=O)(=O)NC(=O)[C@@H](N)CC(O)=O)[C@@H](O)[C@H]2O)C1=O
Canonical SMILES OpenEye OEToolkits 2.0.6 CN1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COS(=O)(=O)NC(=O)[C@H](CC(=O)O)N)O)O

IUPAC InChI

InChI=1S/C14H20N4O11S/c1-17-8(19)2-3-18(14(17)25)13-11(23)10(22)7(29-13)5-28-30(26,27)16-12(24)6(15)4-9(20)21/h2-3,6-7,10-11,13,22-23H,4-5,15H2,1H3,(H,16,24)(H,20,21)/t6-,7+,10+,11+,13+/m0/s1

IUPAC InChI key

ICPNIEAOMPRPLI-MQZAXFGZSA-N
G5Q

wwPDB Information

Atom count

50 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-08-29

Last modified at

2019-12-13

Status

Released

Obsoleted

Not Assigned



G5Q : Atoms of Molecule

Total Number of Atoms: 50
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N1 N N N 0 2.745 2.508 0.624
2 CA C C1 S N N 0 3.374 1.398 -0.105
3 C C C2 N N N 0 2.982 0.091 0.535
4 O O O1 N N N 0 2.572 0.073 1.676
5 CG C C3 N N N 0 5.296 2.799 -0.805
6 CD C C4 N N N 0 4.895 1.554 -0.058
7 OD1 O O2 N N N 0 6.591 3.14 -0.896
8 OD2 O O3 N N N 0 4.451 3.492 -1.323
9 C1' C C5 R N N 0 -2.8 -0.917 0.06
10 C2 C C6 N N N 0 -4.115 1.044 0.637
11 C2' C C7 R N N 0 -2.874 -1.537 -1.359
12 C3' C C8 S N N 0 -2.004 -2.807 -1.204
13 C3U C C9 N N N 0 -5.536 2.905 1.3
14 C4 C C10 N N N 0 -3.542 3.197 -0.067
15 C4' C C11 R N N 0 -1.124 -2.515 0.027
16 C5 C C12 N N N 0 -2.413 2.665 -0.735
17 C5' C C13 N N N 0 0.354 -2.592 -0.359
18 C6 C C14 N N N 0 -2.186 1.335 -0.686
19 N1 N N2 N N N 0 -3.046 0.526 0.006
20 N3 N N3 N N N 0 -4.365 2.366 0.604
21 N3S N N4 N N N 0 3.088 -1.058 -0.161
22 O1S O O4 N N N 0 2.848 -3.498 -0.446
23 O2 O O5 N N N 0 -4.87 0.307 1.242
24 O2' O O6 N N N 0 -4.22 -1.878 -1.698
25 O2S O O7 N N N 0 3.292 -2.525 1.813
26 O3' O O8 N N N 0 -2.827 -3.952 -0.973
27 O4 O O9 N N N 0 -3.766 4.393 -0.097
28 O4' O O10 N N N 0 -1.445 -1.187 0.479
29 O5' O O11 N N N 0 1.161 -2.434 0.81
30 S S S1 N N N 0 2.658 -2.495 0.542
31 H1 H H1 N N N 0 1.74 2.463 0.553
32 H2 H H2 N N N 0 3.039 2.519 1.589
33 H4 H H4 N N N 0 3.039 1.409 -1.143
34 H5 H H5 N N N 0 5.22 1.632 0.979
35 H6 H H6 N N N 0 5.364 0.685 -0.521
36 H7 H H7 N N N 0 6.799 3.947 -1.386
37 H8 H H8 N N N 0 -3.513 -1.402 0.727
38 H9 H H9 N N N 0 -2.447 -0.862 -2.101
39 H10 H H10 N N N 0 -1.384 -2.956 -2.088
40 H11 H H11 N N N 0 -5.262 3.167 2.323
41 H12 H H12 N N N 0 -5.89 3.795 0.78
42 H13 H H13 N N N 0 -6.326 2.155 1.316
43 H14 H H14 N N N 0 -1.339 -3.236 0.816
44 H15 H H15 N N N 0 -1.741 3.315 -1.278
45 H16 H H16 N N N 0 0.561 -3.56 -0.815
46 H17 H H17 N N N 0 0.586 -1.798 -1.069
47 H18 H H18 N N N 0 -1.33 0.911 -1.19
48 H19 H H19 N N N 0 3.415 -1.044 -1.074
49 H20 H H20 N N N 0 -4.317 -2.269 -2.577
50 H21 H H21 N N N 0 -3.441 -4.147 -1.694



G5Q : Chemical Bonds

Total Number of Bonds: 51
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OD2 CG O C doub 1.21 N N
2 CG OD1 C O sing 1.34 N N
3 CG CD C C sing 1.51 N N
4 CD CA C C sing 1.53 N N
5 O3' C3' O C sing 1.43 N N
6 O2' C2' O C sing 1.43 N N
7 C4' C5' C C sing 1.53 N N
8 C4' C3' C C sing 1.54 N N
9 C4' O4' C O sing 1.44 N N
10 C5' O5' C O sing 1.43 N N
11 CA N C N sing 1.47 N N
12 CA C C C sing 1.51 N N
13 C3' C2' C C sing 1.55 N N
14 O4' C1' O C sing 1.44 N N
15 C2' C1' C C sing 1.55 N N
16 C N3S C N sing 1.35 N N
17 C O C O doub 1.21 N N
18 C1' N1 C N sing 1.46 N N
19 N3S S N S sing 1.66 N N
20 O5' S O S sing 1.52 N N
21 O1S S O S doub 1.42 N N
22 O2 C2 O C doub 1.22 N N
23 S O2S S O doub 1.42 N N
24 N1 C2 N C sing 1.35 N N
25 N1 C6 N C sing 1.37 N N
26 C2 N3 C N sing 1.35 N N
27 C6 C5 C C doub 1.35 N N
28 N3 C3U N C sing 1.46 N N
29 N3 C4 N C sing 1.35 N N
30 C5 C4 C C sing 1.42 N N
31 C4 O4 C O doub 1.22 N N
32 N H1 N H sing 1.01 N N
33 N H2 N H sing 1.01 N N
34 CA H4 C H sing 1.09 N N
35 CD H5 C H sing 1.09 N N
36 CD H6 C H sing 1.09 N N
37 OD1 H7 O H sing 0.97 N N
38 C1' H8 C H sing 1.09 N N
39 C2' H9 C H sing 1.09 N N
40 C3' H10 C H sing 1.09 N N
41 C3U H11 C H sing 1.09 N N
42 C3U H12 C H sing 1.09 N N
43 C3U H13 C H sing 1.09 N N
44 C4' H14 C H sing 1.09 N N
45 C5 H15 C H sing 1.08 N N
46 C5' H16 C H sing 1.09 N N
47 C5' H17 C H sing 1.09 N N
48 C6 H18 C H sing 1.08 N N
49 N3S H19 N H sing 0.97 N N
50 O2' H20 O H sing 0.97 N N
51 O3' H21 O H sing 0.97 N N



G5Q : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
G5Q 6hhv Open in New Window Bound ligand 2 1