Chemical Components in the PDB

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GVX : Summary

Code

GVX

One-letter code

X

Molecule name

L-gamma-glutamyl-S-[(2-phenylethyl)carbamothioyl]-L-cysteinylglycine

Systematic names

ProgramVersionName
ACDLabs 12.01 L-gamma-glutamyl-S-[(2-phenylethyl)carbamothioyl]-L-cysteinylglycine
OpenEye OEToolkits 2.0.4 (2~{S})-2-azanyl-5-[[(2~{R})-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-3-(2-phenylethylcarbamothioylsulfanyl)propan-2-yl]amino]-5-oxidanylidene-pentanoic acid

Formula

C19 H26 N4 O6 S2

Formal charge

0

Molecular weight

470.563 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OC(C(CCC(=O)NC(C(=O)NCC(O)=O)CSC(=S)NCCc1ccccc1)N)=O
SMILES CACTVS 3.385 N[CH](CCC(=O)N[CH](CSC(=S)NCCc1ccccc1)C(=O)NCC(O)=O)C(O)=O
SMILES OpenEye OEToolkits 2.0.4 c1ccc(cc1)CCNC(=S)SCC(C(=O)NCC(=O)O)NC(=O)CCC(C(=O)O)N
Canonical SMILES CACTVS 3.385 N[C@@H](CCC(=O)N[C@@H](CSC(=S)NCCc1ccccc1)C(=O)NCC(O)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.4 c1ccc(cc1)CCNC(=S)SC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(=O)O)N

IUPAC InChI

InChI=1S/C19H26N4O6S2/c20-13(18(28)29)6-7-15(24)23-14(17(27)22-10-16(25)26)11-31-19(30)21-9-8-12-4-2-1-3-5-12/h1-5,13-14H,6-11,20H2,(H,21,30)(H,22,27)(H,23,24)(H,25,26)(H,28,29)/t13-,14-/m0/s1

IUPAC InChI key

WSGBVCNCZSZCGE-KBPBESRZSA-N
GVX

wwPDB Information

Atom count

57 (31 without Hydrogen)

Polymer type

Bound ligand

Type description

peptide-like

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-05-05

Last modified at

2016-10-07

Status

Released

Obsoleted

Not Assigned



GVX : Atoms of Molecule

Total Number of Atoms: 57
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O01 O O1 N N N 0 -6.911 4.488 -1.442
2 C02 C C1 N N N 0 -7.068 3.759 -0.326
3 O03 O O2 N N N 0 -8.176 3.439 0.036
4 C04 C C2 S N N 0 -5.863 3.339 0.475
5 N05 N N1 N N N 0 -6.279 2.993 1.841
6 C06 C C3 N N N 0 -5.211 2.121 -0.183
7 C07 C C4 N N N 0 -3.919 1.771 0.558
8 C08 C C5 N N N 0 -3.277 0.572 -0.091
9 O09 O O3 N N N 0 -3.802 0.048 -1.051
10 N10 N N2 N N N 0 -2.121 0.081 0.396
11 C11 C C6 R N N 0 -1.497 -1.085 -0.234
12 C12 C C7 N N N 0 -2.102 -2.345 0.33
13 O13 O O4 N N N 0 -2.968 -2.276 1.176
14 N14 N N3 N N N 0 -1.679 -3.549 -0.105
15 C15 C C8 N N N 0 -2.267 -4.773 0.444
16 C16 C C9 N N N 0 -1.625 -5.973 -0.204
17 O17 O O5 N N N 0 -2.009 -7.211 0.146
18 O18 O O6 N N N 0 -0.765 -5.821 -1.039
19 C19 C C10 N N N 0 0.007 -1.072 0.045
20 S20 S S1 N N N 0 0.734 0.441 -0.634
21 C21 C C11 N N N 0 2.42 0.199 -0.183
22 S22 S S2 N N N 0 2.885 -1.212 0.667
23 N23 N N4 N N N 0 3.343 1.126 -0.507
24 C24 C C12 N N N 0 4.745 0.925 -0.133
25 C25 C C13 N N N 0 5.577 2.115 -0.616
26 C26 C C14 N Y N 0 7.02 1.908 -0.231
27 C27 C C15 N Y N 0 7.878 1.253 -1.093
28 C28 C C16 N Y N 0 9.201 1.064 -0.739
29 C29 C C17 N Y N 0 9.665 1.529 0.477
30 C30 C C18 N Y N 0 8.806 2.185 1.339
31 C31 C C19 N Y N 0 7.485 2.379 0.983
32 H1 H H1 N N N 0 -7.714 4.733 -1.922
33 H2 H H2 N N N 0 -5.146 4.16 0.511
34 H3 H H3 N N N 0 -6.654 3.799 2.32
35 H4 H H4 N N N 0 -6.944 2.234 1.836
36 H6 H H6 N N N 0 -5.896 1.274 -0.138
37 H7 H H7 N N N 0 -4.983 2.35 -1.224
38 H8 H H8 N N N 0 -3.234 2.618 0.513
39 H9 H H9 N N N 0 -4.147 1.543 1.599
40 H10 H H10 N N N 0 -1.701 0.5 1.164
41 H11 H H11 N N N 0 -1.667 -1.051 -1.31
42 H12 H H12 N N N 0 -0.986 -3.604 -0.781
43 H13 H H13 N N N 0 -2.096 -4.807 1.52
44 H14 H H14 N N N 0 -3.339 -4.783 0.246
45 H15 H H15 N N N 0 -1.569 -7.949 -0.297
46 H16 H H16 N N N 0 0.178 -1.106 1.121
47 H17 H H17 N N N 0 0.471 -1.94 -0.424
48 H18 H H18 N N N 0 3.079 1.926 -0.989
49 H19 H H19 N N N 0 4.823 0.844 0.951
50 H20 H H20 N N N 0 5.117 0.01 -0.594
51 H21 H H21 N N N 0 5.499 2.196 -1.7
52 H22 H H22 N N N 0 5.205 3.03 -0.155
53 H23 H H23 N N N 0 7.516 0.889 -2.043
54 H24 H H24 N N N 0 9.872 0.551 -1.413
55 H25 H H25 N N N 0 10.698 1.38 0.753
56 H26 H H26 N N N 0 9.169 2.548 2.289
57 H27 H H27 N N N 0 6.814 2.892 1.656



GVX : Chemical Bonds

Total Number of Bonds: 57
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O18 C16 O C doub 1.21 N N
2 C15 C16 C C sing 1.51 N N
3 C15 N14 C N sing 1.46 N N
4 C16 O17 C O sing 1.34 N N
5 O13 C12 O C doub 1.21 N N
6 N14 C12 N C sing 1.35 N N
7 C12 C11 C C sing 1.51 N N
8 C19 C11 C C sing 1.53 N N
9 C19 S20 C S sing 1.81 N N
10 C11 N10 C N sing 1.46 N N
11 N10 C08 N C sing 1.35 N N
12 C29 C28 C C doub 1.38 N Y
13 C29 C30 C C sing 1.38 N Y
14 C28 C27 C C sing 1.38 N Y
15 S20 C21 S C sing 1.76 N N
16 C08 C07 C C sing 1.51 N N
17 C08 O09 C O doub 1.21 N N
18 C07 C06 C C sing 1.53 N N
19 C30 C31 C C doub 1.38 N Y
20 O03 C02 O C doub 1.21 N N
21 C27 C26 C C doub 1.38 N Y
22 N23 C21 N C sing 1.35 N N
23 N23 C24 N C sing 1.46 N N
24 C21 S22 C S doub 1.71 N N
25 C31 C26 C C sing 1.38 N Y
26 C26 C25 C C sing 1.51 N N
27 C02 C04 C C sing 1.51 N N
28 C02 O01 C O sing 1.34 N N
29 C04 C06 C C sing 1.53 N N
30 C04 N05 C N sing 1.47 N N
31 C24 C25 C C sing 1.53 N N
32 O01 H1 O H sing 0.97 N N
33 C04 H2 C H sing 1.09 N N
34 N05 H3 N H sing 1.01 N N
35 N05 H4 N H sing 1.01 N N
36 C06 H6 C H sing 1.09 N N
37 C06 H7 C H sing 1.09 N N
38 C07 H8 C H sing 1.09 N N
39 C07 H9 C H sing 1.09 N N
40 N10 H10 N H sing 0.97 N N
41 C11 H11 C H sing 1.09 N N
42 N14 H12 N H sing 0.97 N N
43 C15 H13 C H sing 1.09 N N
44 C15 H14 C H sing 1.09 N N
45 O17 H15 O H sing 0.97 N N
46 C19 H16 C H sing 1.09 N N
47 C19 H17 C H sing 1.09 N N
48 N23 H18 N H sing 0.97 N N
49 C24 H19 C H sing 1.09 N N
50 C24 H20 C H sing 1.09 N N
51 C25 H21 C H sing 1.09 N N
52 C25 H22 C H sing 1.09 N N
53 C27 H23 C H sing 1.08 N N
54 C28 H24 C H sing 1.08 N N
55 C29 H25 C H sing 1.08 N N
56 C30 H26 C H sing 1.08 N N
57 C31 H27 C H sing 1.08 N N



GVX : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
GVX 5jcu Open in New Window Bound ligand 4 1
GVX 5jcw Open in New Window Bound ligand 2 1
GVX 6hpe Open in New Window Bound ligand 2 1