Chemical Components in the PDB

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GTB : Summary

Code

GTB

One-letter code

X

Molecule name

S-(P-NITROBENZYL)GLUTATHIONE

Systematic names

ProgramVersionName
ACDLabs 12.01 L-gamma-glutamyl-S-(4-nitrobenzyl)-L-cysteinylglycine
OpenEye OEToolkits 1.7.0 (2S)-2-azanyl-5-[[(2R)-1-(carboxymethylamino)-3-[(4-nitrophenyl)methylsulfanyl]-1-oxo-propan-2-yl]amino]-5-oxo-pentanoic acid

Formula

C17 H22 N4 O8 S

Formal charge

0

Molecular weight

442.444 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=[N+]([O-])c1ccc(cc1)CSCC(C(=O)NCC(=O)O)NC(=O)CCC(C(=O)O)N
SMILES CACTVS 3.370 N[CH](CCC(=O)N[CH](CSCc1ccc(cc1)[N+]([O-])=O)C(=O)NCC(O)=O)C(O)=O
SMILES OpenEye OEToolkits 1.7.0 c1cc(ccc1CSCC(C(=O)NCC(=O)O)NC(=O)CCC(C(=O)O)N)[N+](=O)[O-]
Canonical SMILES CACTVS 3.370 N[C@@H](CCC(=O)N[C@@H](CSCc1ccc(cc1)[N+]([O-])=O)C(=O)NCC(O)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.0 c1cc(ccc1CSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(=O)O)N)[N+](=O)[O-]

IUPAC InChI

InChI=1S/C17H22N4O8S/c18-12(17(26)27)5-6-14(22)20-13(16(25)19-7-15(23)24)9-30-8-10-1-3-11(4-2-10)21(28)29/h1-4,12-13H,5-9,18H2,(H,19,25)(H,20,22)(H,23,24)(H,26,27)/t12-,13-/m0/s1

IUPAC InChI key

OAWORKDPTSAMBZ-STQMWFEESA-N
GTB

wwPDB Information

Atom count

52 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



GTB : Atoms of Molecule

Total Number of Atoms: 52
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 0 -4.418 4.276 1.643
2 CA1 C CA1 S N N 0 -3.669 4.453 0.392
3 C1 C C1 N N N 0 -4.457 5.331 -0.546
4 O11 O O11 N N N 0 -5.647 5.47 -0.387
5 O12 O O12 N N N 0 -3.838 5.958 -1.558
6 CB1 C CB1 N N N 0 -3.436 3.089 -0.261
7 CG1 C CG1 N N N 0 -2.532 2.242 0.636
8 CD1 C CD1 N N N 0 -2.303 0.898 -0.0070
9 OE1 O OE1 N N N 0 -2.812 0.643 -1.077
10 N2 N N2 N N N 0 -1.531 -0.02 0.608
11 CA2 C CA2 R N N 0 -1.308 -1.326 -0.017
12 C2 C C2 N N N 0 -2.442 -2.253 0.338
13 O2 O O2 N N N 0 -3.347 -1.861 1.044
14 CB2 C CB2 N N N 0 0.01 -1.916 0.489
15 SG2 S SG2 N N N 0 1.375 -0.8 0.062
16 N3 N N3 N N N 0 -2.45 -3.517 -0.129
17 CA3 C CA3 N N N 0 -3.553 -4.418 0.217
18 C3 C C3 N N N 0 -3.323 -5.762 -0.426
19 O31 O O31 N N N 0 -2.34 -5.948 -1.103
20 O32 O O32 N N N 0 -4.212 -6.752 -0.247
21 C' C C' N N N 0 2.827 -1.656 0.733
22 C1' C C1' N Y N 0 4.064 -0.841 0.454
23 C2' C C2' N Y N 0 4.488 0.106 1.367
24 C3' C C3' N Y N 0 5.622 0.854 1.111
25 C4' C C4' N Y N 0 6.333 0.653 -0.057
26 N41 N N41 N N N 1 7.548 1.453 -0.332
27 O41 O O41 N N N -1 7.921 2.289 0.472
28 O42 O O42 N N N 0 8.174 1.277 -1.361
29 C5' C C5' N Y N 0 5.91 -0.296 -0.97
30 C6' C C6' N Y N 0 4.777 -1.045 -0.712
31 HN11 H HN11 N N N 0 -4.529 5.155 2.125
32 HN12 H HN12 N N N 0 -5.313 3.843 1.47
33 HA1 H HA1 N N N 0 -2.709 4.922 0.607
34 HB11 H HB11 N N N 0 -4.392 2.582 -0.395
35 HB12 H HB12 N N N 0 -2.959 3.227 -1.231
36 HG11 H HG11 N N N 0 -1.576 2.748 0.77
37 HG12 H HG12 N N N 0 -3.009 2.104 1.607
38 HN2 H HN2 N N N 0 -1.123 0.184 1.464
39 HA2 H HA2 N N N 0 -1.261 -1.208 -1.1
40 HB21 H HB21 N N N 0 -0.037 -2.034 1.572
41 HB22 H HB22 N N N 0 0.176 -2.887 0.024
42 HN3 H HN3 N N N 0 -1.726 -3.831 -0.693
43 HA31 H HA31 N N N 0 -3.6 -4.537 1.299
44 HA32 H HA32 N N N 0 -4.492 -3.998 -0.144
45 H'1 H H'1 N N N 0 2.709 -1.781 1.81
46 H'2 H H'2 N N N 0 2.922 -2.634 0.262
47 H2' H H2' N N N 0 3.933 0.263 2.28
48 H3' H H3' N N N 0 5.953 1.594 1.824
49 H5' H H5' N N N 0 6.465 -0.452 -1.883
50 H6' H H6' N N N 0 4.448 -1.789 -1.423
51 HO1 H HO1 N N N 0 -4.385 6.51 -2.133
52 HO3 H HO3 N N N 0 -4.022 -7.596 -0.679



GTB : Chemical Bonds

Total Number of Bonds: 52
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 CA1 N C sing 1.47 N N
2 N1 HN11 N H sing 1.01 N N
3 N1 HN12 N H sing 1.01 N N
4 CA1 C1 C C sing 1.51 N N
5 CA1 CB1 C C sing 1.53 N N
6 CA1 HA1 C H sing 1.09 N N
7 C1 O11 C O doub 1.21 N N
8 C1 O12 C O sing 1.34 N N
9 CB1 CG1 C C sing 1.53 N N
10 CB1 HB11 C H sing 1.09 N N
11 CB1 HB12 C H sing 1.09 N N
12 CG1 CD1 C C sing 1.51 N N
13 CG1 HG11 C H sing 1.09 N N
14 CG1 HG12 C H sing 1.09 N N
15 CD1 OE1 C O doub 1.21 N N
16 CD1 N2 C N sing 1.35 N N
17 N2 CA2 N C sing 1.46 N N
18 N2 HN2 N H sing 0.97 N N
19 CA2 C2 C C sing 1.51 N N
20 CA2 CB2 C C sing 1.53 N N
21 CA2 HA2 C H sing 1.09 N N
22 C2 O2 C O doub 1.21 N N
23 C2 N3 C N sing 1.35 N N
24 CB2 SG2 C S sing 1.81 N N
25 CB2 HB21 C H sing 1.09 N N
26 CB2 HB22 C H sing 1.09 N N
27 SG2 C' S C sing 1.81 N N
28 N3 CA3 N C sing 1.47 N N
29 N3 HN3 N H sing 0.97 N N
30 CA3 C3 C C sing 1.51 N N
31 CA3 HA31 C H sing 1.09 N N
32 CA3 HA32 C H sing 1.09 N N
33 C3 O31 C O doub 1.21 N N
34 C3 O32 C O sing 1.34 N N
35 C' C1' C C sing 1.51 N N
36 C' H'1 C H sing 1.09 N N
37 C' H'2 C H sing 1.09 N N
38 C1' C2' C C doub 1.38 N Y
39 C1' C6' C C sing 1.38 N Y
40 C2' C3' C C sing 1.38 N Y
41 C2' H2' C H sing 1.08 N N
42 C3' C4' C C doub 1.38 N Y
43 C3' H3' C H sing 1.08 N N
44 C4' N41 C N sing 1.48 N N
45 C4' C5' C C sing 1.38 N Y
46 N41 O41 N O sing 1.22 N N
47 N41 O42 N O doub 1.22 N N
48 C5' C6' C C doub 1.38 N Y
49 C5' H5' C H sing 1.08 N N
50 C6' H6' C H sing 1.08 N N
51 O12 HO1 O H sing 0.97 N N
52 O32 HO3 O H sing 0.97 N N



GTB : Used in PDB Entries

Total Number of PDB Entries: 10
Ligand Code PDB Entry ID Type Total Distinct
GTB 1glq Open in New Window Bound ligand 2 1
GTB 1gti Open in New Window Bound ligand 6 1
GTB 1k0c Open in New Window Bound ligand 3 1
GTB 2oac Open in New Window Bound ligand 2 1
GTB 2oad Open in New Window Bound ligand 2 1
GTB 2qmc Open in New Window Bound ligand 2 1
GTB 2vo4 Open in New Window Bound ligand 2 1
GTB 2ycd Open in New Window Bound ligand 1 1
GTB 3o76 Open in New Window Bound ligand 2 1
GTB 5agy Open in New Window Bound ligand 2 1