Chemical Components in the PDB

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VDW : Summary

Code

VDW

One-letter code

X

Molecule name

[(2~{S})-5-[[(2~{R})-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-3-sulfanyl-propan-2-yl]amino]-1-oxidanyl-1,5-bis(oxidanylidene)pentan-2-yl]azanium

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 [(2~{S})-5-[[(2~{R})-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-3-sulfanyl-propan-2-yl]amino]-1-oxidanyl-1,5-bis(oxidanylidene)pentan-2-yl]azanium

Formula

C10 H18 N3 O6 S

Formal charge

1

Molecular weight

308.331 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 [NH3+][CH](CCC(=O)N[CH](CS)C(=O)NCC(O)=O)C(O)=O
SMILES OpenEye OEToolkits 2.0.7 C(CC(=O)NC(CS)C(=O)NCC(=O)O)C(C(=O)O)[NH3+]
Canonical SMILES CACTVS 3.385 [NH3+][C@@H](CCC(=O)N[C@@H](CS)C(=O)NCC(O)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 C(CC(=O)N[C@@H](CS)C(=O)NCC(=O)O)[C@@H](C(=O)O)[NH3+]

IUPAC InChI

InChI=1S/C10H17N3O6S/c11-5(10(18)19)1-2-7(14)13-6(4-20)9(17)12-3-8(15)16/h5-6,20H,1-4,11H2,(H,12,17)(H,13,14)(H,15,16)(H,18,19)/p+1/t5-,6-/m0/s1

IUPAC InChI key

RWSXRVCMGQZWBV-WDSKDSINSA-O
VDW

wwPDB Information

Atom count

38 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-05-07

Last modified at

2021-05-21

Status

Released

Obsoleted

Not Assigned



VDW : Atoms of Molecule

Total Number of Atoms: 38
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 1 -4.751 2.226 -0.17
2 CA1 C C1 S N N 0 -4.783 0.775 -0.396
3 C1 C C2 N N N 0 -5.992 0.187 0.283
4 O11 O O1 N N N 0 -6.542 0.796 1.171
5 O12 O O2 N N N 0 -6.459 -1.012 -0.097
6 CB1 C C3 N N N 0 -3.515 0.141 0.181
7 CG1 C C4 N N N 0 -2.296 0.645 -0.594
8 CD1 C C5 N N N 0 -1.047 0.021 -0.025
9 OE1 O O3 N N N 0 -1.125 -0.751 0.907
10 N2 N N2 N N N 0 0.156 0.32 -0.553
11 CA2 C C6 R N N 0 1.37 -0.287 -0.001
12 C2 C C7 N N N 0 2.552 0.602 -0.29
13 O2 O O4 N N N 0 2.396 1.64 -0.898
14 CB2 C C8 N N N 0 1.593 -1.657 -0.643
15 SG2 S S1 N N N 0 0.169 -2.727 -0.295
16 N3 N N3 N N N 0 3.783 0.243 0.126
17 CA3 C C9 N N N 0 4.932 1.107 -0.155
18 C3 C C10 N N N 0 6.181 0.483 0.413
19 O31 O O5 N N N 0 6.117 -0.575 0.994
20 O32 O O6 N N N 0 7.363 1.102 0.275
21 HN13 H H1 N N N 0 -3.941 2.62 -0.626
22 HN11 H H2 N N N 0 -5.587 2.644 -0.551
23 HN12 H H3 N N N 0 -4.703 2.411 0.82
24 HA1 H H4 N N N 0 -4.834 0.575 -1.467
25 H1 H H5 N N N 0 -7.238 -1.348 0.368
26 HB13 H H6 N N N 0 -3.418 0.416 1.231
27 HB12 H H7 N N N 0 -3.579 -0.943 0.093
28 HG13 H H8 N N N 0 -2.393 0.371 -1.644
29 HG12 H H9 N N N 0 -2.232 1.73 -0.506
30 HN2 H H10 N N N 0 0.219 0.937 -1.299
31 HA2 H H11 N N N 0 1.259 -0.404 1.077
32 HB23 H H12 N N N 0 1.704 -1.539 -1.721
33 HB22 H H13 N N N 0 2.496 -2.109 -0.232
34 HSG H H14 N N N 0 0.498 -3.877 -0.909
35 HN3 H H15 N N N 0 3.907 -0.587 0.613
36 HA31 H H16 N N N 0 5.043 1.225 -1.233
37 HA32 H H17 N N N 0 4.773 2.083 0.303
38 H2 H H18 N N N 0 8.136 0.663 0.656



VDW : Chemical Bonds

Total Number of Bonds: 37
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 SG2 CB2 S C sing 1.81 N N
2 CB2 CA2 C C sing 1.53 N N
3 CA2 N2 C N sing 1.47 N N
4 CA2 C2 C C sing 1.51 N N
5 N2 CD1 N C sing 1.35 N N
6 O11 C1 O C doub 1.21 N N
7 CG1 CD1 C C sing 1.51 N N
8 CG1 CB1 C C sing 1.53 N N
9 O12 C1 O C sing 1.34 N N
10 CD1 OE1 C O doub 1.21 N N
11 C1 CA1 C C sing 1.51 N N
12 N1 CA1 N C sing 1.47 N N
13 C2 N3 C N sing 1.35 N N
14 C2 O2 C O doub 1.21 N N
15 N3 CA3 N C sing 1.46 N N
16 CA1 CB1 C C sing 1.53 N N
17 CA3 C3 C C sing 1.51 N N
18 C3 O31 C O doub 1.21 N N
19 C3 O32 C O sing 1.34 N N
20 N1 HN13 N H sing 1.01 N N
21 N1 HN11 N H sing 1.01 N N
22 N1 HN12 N H sing 1.01 N N
23 CA1 HA1 C H sing 1.09 N N
24 O12 H1 O H sing 0.97 N N
25 CB1 HB13 C H sing 1.09 N N
26 CB1 HB12 C H sing 1.09 N N
27 CG1 HG13 C H sing 1.09 N N
28 CG1 HG12 C H sing 1.09 N N
29 N2 HN2 N H sing 0.97 N N
30 CA2 HA2 C H sing 1.09 N N
31 CB2 HB23 C H sing 1.09 N N
32 CB2 HB22 C H sing 1.09 N N
33 SG2 HSG S H sing 1.34 N N
34 N3 HN3 N H sing 0.97 N N
35 CA3 HA31 C H sing 1.09 N N
36 CA3 HA32 C H sing 1.09 N N
37 O32 H2 O H sing 0.97 N N



VDW : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
VDW 6tk8 Open in New Window Bound ligand 1 1
VDW 7odm Open in New Window Bound ligand 1 1