Chemical Components in the PDB

pdbe.org/chem
spacer

1G5 : Summary

Code

1G5

One-letter code

X

Molecule name

HMB-Val-Ser-Phe(4-NH2CH2)-methyl vinyl sulfone, bound form

Systematic names

ProgramVersionName
ACDLabs 12.01 N-(3-hydroxy-2-methylbenzoyl)-L-valyl-N-[(2S)-1-[4-(aminomethyl)phenyl]-4-(methylsulfonyl)butan-2-yl]-L-serinamide
OpenEye OEToolkits 1.7.6 N-[(2S)-1-[[(2S)-1-[[(2S)-1-[4-(aminomethyl)phenyl]-4-methylsulfonyl-butan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-3-methyl-1-oxidanylidene-butan-2-yl]-2-methyl-3-oxidanyl-benzamide

Formula

C28 H40 N4 O7 S

Formal charge

0

Molecular weight

576.705 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=S(=O)(C)CCC(NC(=O)C(NC(=O)C(NC(=O)c1cccc(O)c1C)C(C)C)CO)Cc2ccc(cc2)CN
SMILES CACTVS 3.370 CC(C)[CH](NC(=O)c1cccc(O)c1C)C(=O)N[CH](CO)C(=O)N[CH](CC[S](C)(=O)=O)Cc2ccc(CN)cc2
SMILES OpenEye OEToolkits 1.7.6 Cc1c(cccc1O)C(=O)NC(C(C)C)C(=O)NC(CO)C(=O)NC(CCS(=O)(=O)C)Cc2ccc(cc2)CN
Canonical SMILES CACTVS 3.370 CC(C)[C@H](NC(=O)c1cccc(O)c1C)C(=O)N[C@@H](CO)C(=O)N[C@H](CC[S](C)(=O)=O)Cc2ccc(CN)cc2
Canonical SMILES OpenEye OEToolkits 1.7.6 Cc1c(cccc1O)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CO)C(=O)N[C@H](CCS(=O)(=O)C)Cc2ccc(cc2)CN

IUPAC InChI

InChI=1S/C28H40N4O7S/c1-17(2)25(32-26(35)22-6-5-7-24(34)18(22)3)28(37)31-23(16-33)27(36)30-21(12-13-40(4,38)39)14-19-8-10-20(15-29)11-9-19/h5-11,17,21,23,25,33-34H,12-16,29H2,1-4H3,(H,30,36)(H,31,37)(H,32,35)/t21-,23+,25+/m1/s1

IUPAC InChI key

OCEOTFNCOHQGQA-VTZPFEBOSA-N

Has sub-components

PF0 , VAL , SER , 1G3
1G5

wwPDB Information

Atom count

80 (40 without Hydrogen)

Polymer type

Amino Acid

Type description

peptide-like

Type code

ATOMP

Is modified

No

Standard parent

Not Assigned

Defined at

2013-01-22

Last modified at

2013-01-25

Status

Released

Obsoleted

Not Assigned



1G5 : Atoms of Molecule

Total Number of Atoms: 80
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 8.665 1.297 -1.101
2 C11 C C11 S N N 0 2.648 -0.623 0.414
3 C12 C C12 N N N 0 2.387 -0.27 1.879
4 C13 C C13 N N N 0 3.554 -0.763 2.738
5 C14 C C14 N N N 0 2.253 1.247 2.023
6 C15 C C15 N N N 0 1.499 -0.138 -0.432
7 C18 C C18 S N N 0 -0.864 -0.126 -1.025
8 C19 C C19 N N N 0 -2.15 -0.262 -0.251
9 C2 C C2 N Y N 0 8.727 0.137 -0.34
10 C21 C C21 S N N 0 -4.567 -0.019 -0.058
11 C22 C C22 N N N 0 -5.591 0.985 -0.59
12 C23 C C23 N N N 0 -5.113 -1.439 -0.222
13 C24 C C24 N Y N 0 -5.108 2.387 -0.318
14 C25 C C25 N Y N 0 -5.442 3.015 0.867
15 C26 C C26 N Y N 0 -4.999 4.301 1.117
16 C27 C C27 N Y N 0 -4.221 4.957 0.182
17 C28 C C28 N Y N 0 -3.886 4.328 -1.003
18 C29 C C29 N Y N 0 -4.325 3.041 -1.251
19 C3 C C3 N Y N 0 7.561 -0.478 0.083
20 C30 C C30 N N N 0 -3.738 6.359 0.454
21 C35 C C35 N N N 0 -4.146 -2.435 0.422
22 C39 C C39 N N N 0 -3.514 -5.109 1.046
23 C4 C C4 N Y N 0 6.324 0.072 -0.258
24 C40 C C40 N N N 0 -0.947 -0.965 -2.302
25 C5 C C5 N Y N 0 6.272 1.239 -1.023
26 C6 C C6 N Y N 0 7.441 1.843 -1.439
27 C7 C C7 N N N 0 7.626 -1.737 0.908
28 C9 C C9 N N N 0 5.074 -0.577 0.19
29 H1 H H1 N N N 0 7.51 -2.604 0.258
30 H10 H H10 N N N 0 1.466 -0.749 2.21
31 H11 H H11 N N N 0 3.368 -0.512 3.782
32 H12 H H12 N N N 0 3.65 -1.844 2.635
33 H13 H H13 N N N 0 4.476 -0.284 2.407
34 H14 H H14 N N N 0 1.422 1.598 1.411
35 H15 H H15 N N N 0 2.067 1.498 3.067
36 H16 H H16 N N N 0 3.175 1.726 1.692
37 H17 H H17 N N N 0 0.096 -1.241 0.506
38 H18 H H18 N N N 0 -0.707 0.92 -1.287
39 H19 H H19 N N N 0 -1.721 -0.559 -2.954
40 H2 H H2 N N N 0 8.589 -1.789 1.415
41 H20 H H20 N N N 0 0.013 -0.938 -2.818
42 H21 H H21 N N N 0 -1.339 -2.906 -2.728
43 H22 H H22 N N N 0 -3.329 0.47 -1.713
44 H23 H H23 N N N 0 -4.378 0.178 0.997
45 H24 H H24 N N N 0 -5.218 -1.668 -1.282
46 H25 H H25 N N N 0 -6.086 -1.512 0.264
47 H26 H H26 N N N 0 -4.041 -2.206 1.482
48 H27 H H27 N N N 0 -3.173 -2.362 -0.064
49 H28 H H28 N N N 0 -2.559 -4.957 0.542
50 H29 H H29 N N N 0 -3.427 -4.801 2.089
51 H3 H H3 N N N 0 6.826 -1.728 1.648
52 H30 H H30 N N N 0 -3.785 -6.163 1.0
53 H31 H H31 N N N 0 -5.714 0.845 -1.664
54 H32 H H32 N N N 0 -6.547 0.828 -0.091
55 H33 H H33 N N N 0 -6.05 2.502 1.598
56 H34 H H34 N N N 0 -5.261 4.792 2.042
57 H35 H H35 N N N 0 -3.632 6.896 -0.489
58 H36 H H36 N N N 0 -4.459 6.875 1.087
59 H37 H H37 N N N 0 -2.092 7.232 1.329
60 H38 H H38 N N N 0 -2.495 5.756 1.981
61 H4 H H4 N N N 0 10.298 -0.068 0.818
62 H40 H H40 N N N 0 -3.277 4.841 -1.733
63 H41 H H41 N N N 0 -4.06 2.549 -2.174
64 H5 H H5 N N N 0 9.576 1.772 -1.433
65 H6 H H6 N N N 0 7.399 2.745 -2.031
66 H7 H H7 N N N 0 5.318 1.668 -1.289
67 H8 H H8 N N N 0 3.853 0.878 -0.484
68 H9 H H9 N N N 0 2.744 -1.704 0.311
69 N10 N N10 N N N 0 3.887 0.021 -0.031
70 N17 N N17 N N N 0 0.253 -0.598 -0.203
71 N20 N N20 N N N 0 -3.317 0.113 -0.811
72 N31 N N31 N N N 0 -2.438 6.304 1.135
73 O16 O O16 N N N 0 1.695 0.666 -1.318
74 O32 O O32 N N N 0 5.117 -1.651 0.758
75 O33 O O33 N N N 0 -2.135 -0.709 0.877
76 O37 O O37 N N N 0 -5.998 -4.229 0.974
77 O38 O O38 N N N 0 -4.803 -4.444 -1.155
78 O41 O O41 N N N 0 -1.27 -2.316 -1.965
79 O8 O O8 N N N 0 9.933 -0.398 -0.014
80 S36 S S36 N N N 0 -4.794 -4.118 0.228



1G5 : Chemical Bonds

Total Number of Bonds: 81
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C35 C23 C C sing 1.53 N N
2 C35 S36 C S sing 1.81 N N
3 C23 C21 C C sing 1.53 N N
4 O37 S36 O S doub 1.42 N N
5 C22 C21 C C sing 1.53 N N
6 C22 C24 C C sing 1.51 N N
7 S36 C39 S C sing 1.81 N N
8 S36 O38 S O doub 1.42 N N
9 C25 C24 C C doub 1.38 N Y
10 C25 C26 C C sing 1.38 N Y
11 C21 N20 C N sing 1.47 N N
12 C24 C29 C C sing 1.38 N Y
13 C26 C27 C C doub 1.38 N Y
14 C29 C28 C C doub 1.38 N Y
15 N20 C19 N C sing 1.35 N N
16 C27 C28 C C sing 1.38 N Y
17 C27 C30 C C sing 1.51 N N
18 N31 C30 N C sing 1.47 N N
19 C19 O33 C O doub 1.21 N N
20 C19 C18 C C sing 1.51 N N
21 C18 C40 C C sing 1.53 N N
22 C18 N17 C N sing 1.46 N N
23 C40 O41 C O sing 1.43 N N
24 N17 C15 N C sing 1.35 N N
25 C14 C12 C C sing 1.53 N N
26 C15 O16 C O doub 1.21 N N
27 C15 C11 C C sing 1.51 N N
28 C12 C11 C C sing 1.53 N N
29 C12 C13 C C sing 1.53 N N
30 C11 N10 C N sing 1.47 N N
31 N10 C9 N C sing 1.35 N N
32 O32 C9 O C doub 1.22 N N
33 C9 C4 C C sing 1.48 N N
34 C5 C4 C C doub 1.4 N Y
35 C5 C6 C C sing 1.38 N Y
36 C4 C3 C C sing 1.4 N Y
37 C6 C1 C C doub 1.38 N Y
38 C3 C7 C C sing 1.51 N N
39 C3 C2 C C doub 1.38 N Y
40 C1 C2 C C sing 1.39 N Y
41 C2 O8 C O sing 1.36 N N
42 C7 H1 C H sing 1.09 N N
43 C7 H2 C H sing 1.09 N N
44 C7 H3 C H sing 1.09 N N
45 O8 H4 O H sing 0.97 N N
46 C1 H5 C H sing 1.08 N N
47 C6 H6 C H sing 1.08 N N
48 C5 H7 C H sing 1.08 N N
49 N10 H8 N H sing 0.97 N N
50 C11 H9 C H sing 1.09 N N
51 C12 H10 C H sing 1.09 N N
52 C13 H11 C H sing 1.09 N N
53 C13 H12 C H sing 1.09 N N
54 C13 H13 C H sing 1.09 N N
55 C14 H14 C H sing 1.09 N N
56 C14 H15 C H sing 1.09 N N
57 C14 H16 C H sing 1.09 N N
58 N17 H17 N H sing 0.97 N N
59 C18 H18 C H sing 1.09 N N
60 C40 H19 C H sing 1.09 N N
61 C40 H20 C H sing 1.09 N N
62 O41 H21 O H sing 0.97 N N
63 N20 H22 N H sing 0.97 N N
64 C21 H23 C H sing 1.09 N N
65 C23 H24 C H sing 1.09 N N
66 C23 H25 C H sing 1.09 N N
67 C35 H26 C H sing 1.09 N N
68 C35 H27 C H sing 1.09 N N
69 C39 H28 C H sing 1.09 N N
70 C39 H29 C H sing 1.09 N N
71 C39 H30 C H sing 1.09 N N
72 C22 H31 C H sing 1.09 N N
73 C22 H32 C H sing 1.09 N N
74 C25 H33 C H sing 1.08 N N
75 C26 H34 C H sing 1.08 N N
76 C30 H35 C H sing 1.09 N N
77 C30 H36 C H sing 1.09 N N
78 N31 H37 N H sing 1.01 N N
79 N31 H38 N H sing 1.01 N N
80 C28 H40 C H sing 1.08 N N
81 C29 H41 C H sing 1.08 N N



1G5 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
1G5 4int Open in New Window Bound ligand 4 1