Chemical Components in the PDB

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BO9 : Summary

Code

BO9

One-letter code

X

Molecule name

N1-[(1R)-1-(DIHYDROXYBORYL)ETHYL]-N2-[(TERT-BUTOXYCARBONYL)-D-GAMMA-GLUTAMYL]-N6-[(BENZYLOXY)CARBONYL-L-LYSINAMIDE

Systematic names

ProgramVersionName
ACDLabs 10.04 N-(tert-butoxycarbonyl)-L-gamma-glutamyl-N~6~-[(benzyloxy)carbonyl]-N-[(1S)-1-(dihydroxyboranyl)ethyl]-L-lysinamide
OpenEye OEToolkits 1.5.0 (2S)-5-[[(2S)-1-[[(1S)-1-(dihydroxyboranyl)ethyl]amino]-1-oxo-6-phenylmethoxycarbonylamino-hexan-2-yl]amino]-2-[(2-methylpropan-2-yl)oxycarbonylamino]-5-oxo-pentanoic acid

Formula

C26 H41 B N4 O10

Formal charge

0

Molecular weight

580.436 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(OC(C)(C)C)NC(C(=O)O)CCC(=O)NC(C(=O)NC(B(O)O)C)CCCCNC(=O)OCc1ccccc1
SMILES CACTVS 3.341 C[CH](NC(=O)[CH](CCCCNC(=O)OCc1ccccc1)NC(=O)CC[CH](NC(=O)OC(C)(C)C)C(O)=O)B(O)O
SMILES OpenEye OEToolkits 1.5.0 B(C(C)NC(=O)C(CCCCNC(=O)OCc1ccccc1)NC(=O)CCC(C(=O)O)NC(=O)OC(C)(C)C)(O)O
Canonical SMILES CACTVS 3.341 C[C@@H](NC(=O)[C@H](CCCCNC(=O)OCc1ccccc1)NC(=O)CC[C@H](NC(=O)OC(C)(C)C)C(O)=O)B(O)O
Canonical SMILES OpenEye OEToolkits 1.5.0 B([C@@H](C)NC(=O)[C@H](CCCCNC(=O)OCc1ccccc1)NC(=O)CC[C@@H](C(=O)O)NC(=O)OC(C)(C)C)(O)O

IUPAC InChI

InChI=1S/C26H41BN4O10/c1-17(27(38)39)29-22(33)19(12-8-9-15-28-24(36)40-16-18-10-6-5-7-11-18)30-21(32)14-13-20(23(34)35)31-25(37)41-26(2,3)4/h5-7,10-11,17,19-20,38-39H,8-9,12-16H2,1-4H3,(H,28,36)(H,29,33)(H,30,32)(H,31,37)(H,34,35)/t17-,19+,20+/m1/s1

IUPAC InChI key

OTTYWVUOPWENAJ-HOJAQTOUSA-N
BO9

wwPDB Information

Atom count

82 (41 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2005-04-18

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



BO9 : Atoms of Molecule

Total Number of Atoms: 82
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O36 O O36 N N N 0 -5.609 -3.955 0.161
2 C35 C C35 N N N 0 -5.885 -2.901 -0.377
3 O37 O O37 N N N 0 -6.516 -2.897 -1.566
4 C38 C C38 N N N 0 -6.866 -4.152 -2.206
5 C41 C C41 N N N 0 -7.803 -4.946 -1.294
6 C40 C C40 N N N 0 -7.569 -3.868 -3.535
7 C39 C C39 N N N 0 -5.596 -4.965 -2.465
8 N34 N N34 N N N 0 -5.56 -1.736 0.218
9 C30 C C30 S N N 0 -4.873 -1.741 1.512
10 C31 C C31 N N N 0 -5.889 -1.855 2.619
11 O33 O O33 N N N 0 -7.066 -1.926 2.354
12 O32 O O32 N N N 0 -5.487 -1.879 3.899
13 C29 C C29 N N N 0 -4.085 -0.44 1.676
14 C28 C C28 N N N 0 -2.972 -0.382 0.628
15 C26 C C26 N N N 0 -2.195 0.899 0.789
16 O27 O O27 N N N 0 -2.502 1.689 1.657
17 N25 N N25 N N N 0 -1.16 1.168 -0.031
18 C9 C C9 S N N 0 -0.405 2.413 0.126
19 C7 C C7 N N N 0 -1.1 3.52 -0.625
20 O8 O O8 N N N 0 -2.125 3.29 -1.232
21 N6 N N6 N N N 0 -0.583 4.764 -0.623
22 C4 C C4 S N N 0 -1.258 5.84 -1.353
23 C5 C C5 N N N 0 -0.226 6.645 -2.145
24 B1 B B1 N N N 0 -1.99 6.785 -0.335
25 O3 O O3 N N N 0 -3.333 6.519 0.041
26 O2 O O2 N N N 0 -1.308 7.905 0.21
27 C10 C C10 N N N 0 1.007 2.227 -0.432
28 C11 C C11 N N N 0 1.756 1.192 0.41
29 C12 C C12 N N N 0 3.168 1.006 -0.147
30 C13 C C13 N N N 0 3.917 -0.03 0.695
31 N14 N N14 N N N 0 5.269 -0.208 0.161
32 C15 C C15 N N N 0 6.116 -1.077 0.747
33 O16 O O16 N N N 0 5.757 -1.714 1.718
34 O17 O O17 N N N 0 7.359 -1.241 0.256
35 C18 C C18 N N N 0 8.271 -2.178 0.888
36 C19 C C19 N Y N 0 9.586 -2.172 0.152
37 C24 C C24 N Y N 0 10.587 -1.298 0.532
38 C23 C C23 N Y N 0 11.793 -1.293 -0.143
39 C22 C C22 N Y N 0 11.999 -2.162 -1.198
40 C21 C C21 N Y N 0 10.998 -3.037 -1.578
41 C20 C C20 N Y N 0 9.793 -3.045 -0.9
42 H411 H 1H41 N N N 0 -8.708 -4.367 -1.11
43 H412 H 2H41 N N N 0 -8.067 -5.888 -1.775
44 H413 H 3H41 N N N 0 -7.303 -5.148 -0.347
45 H401 H 1H40 N N N 0 -6.901 -3.302 -4.186
46 H402 H 2H40 N N N 0 -7.832 -4.81 -4.016
47 H403 H 3H40 N N N 0 -8.474 -3.288 -3.352
48 H391 H 1H39 N N N 0 -5.096 -5.168 -1.518
49 H392 H 2H39 N N N 0 -5.859 -5.907 -2.945
50 H393 H 3H39 N N N 0 -4.929 -4.4 -3.115
51 H34 H H34 N N N 0 -5.78 -0.895 -0.211
52 H30 H H30 N N N 0 -4.189 -2.588 1.558
53 H32 H H32 N N N 0 -6.139 -1.953 4.61
54 H291 H 1H29 N N N 0 -3.647 -0.404 2.673
55 H292 H 2H29 N N N 0 -4.754 0.41 1.542
56 H281 H 1H28 N N N 0 -3.41 -0.419 -0.37
57 H282 H 2H28 N N N 0 -2.302 -1.232 0.762
58 H25 H H25 N N N 0 -0.915 0.536 -0.725
59 H9 H H9 N N N 0 -0.348 2.672 1.183
60 HN6 H HN6 N N N 0 0.237 4.948 -0.138
61 H4 H H4 N N N 0 -1.988 5.41 -2.039
62 H51 H 1H5 N N N 0 0.504 7.074 -1.459
63 H52 H 2H5 N N N 0 0.282 5.989 -2.852
64 H53 H 3H5 N N N 0 -0.729 7.445 -2.688
65 HO3 H HO3 N N N 0 -3.605 5.723 -0.436
66 HO2 H HO2 N N N 0 -1.928 8.347 0.805
67 H101 H 1H10 N N N 0 0.948 1.882 -1.464
68 H102 H 2H10 N N N 0 1.54 3.178 -0.396
69 H111 H 1H11 N N N 0 1.815 1.537 1.442
70 H112 H 2H11 N N N 0 1.223 0.241 0.375
71 H121 H 1H12 N N N 0 3.109 0.661 -1.179
72 H122 H 2H12 N N N 0 3.701 1.956 -0.112
73 H131 H 1H13 N N N 0 3.976 0.316 1.727
74 H132 H 2H13 N N N 0 3.384 -0.98 0.659
75 H14 H H14 N N N 0 5.555 0.3 -0.614
76 H181 H 1H18 N N N 0 8.434 -1.884 1.925
77 H182 H 2H18 N N N 0 7.842 -3.179 0.857
78 H24 H H24 N N N 0 10.427 -0.619 1.356
79 H23 H H23 N N N 0 12.575 -0.61 0.154
80 H22 H H22 N N N 0 12.941 -2.157 -1.726
81 H21 H H21 N N N 0 11.158 -3.715 -2.403
82 H20 H H20 N N N 0 9.011 -3.728 -1.197



BO9 : Chemical Bonds

Total Number of Bonds: 82
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O36 C35 O C doub 1.22 N N
2 C35 O37 C O sing 1.35 N N
3 C35 N34 C N sing 1.35 N N
4 O37 C38 O C sing 1.45 N N
5 C38 C41 C C sing 1.53 N N
6 C38 C40 C C sing 1.53 N N
7 C38 C39 C C sing 1.53 N N
8 C41 H411 C H sing 1.09 N N
9 C41 H412 C H sing 1.09 N N
10 C41 H413 C H sing 1.09 N N
11 C40 H401 C H sing 1.09 N N
12 C40 H402 C H sing 1.09 N N
13 C40 H403 C H sing 1.09 N N
14 C39 H391 C H sing 1.09 N N
15 C39 H392 C H sing 1.09 N N
16 C39 H393 C H sing 1.09 N N
17 N34 C30 N C sing 1.47 N N
18 N34 H34 N H sing 0.97 N N
19 C30 C31 C C sing 1.51 N N
20 C30 C29 C C sing 1.53 N N
21 C30 H30 C H sing 1.09 N N
22 C31 O33 C O doub 1.21 N N
23 C31 O32 C O sing 1.34 N N
24 O32 H32 O H sing 0.97 N N
25 C29 C28 C C sing 1.53 N N
26 C29 H291 C H sing 1.09 N N
27 C29 H292 C H sing 1.09 N N
28 C28 C26 C C sing 1.51 N N
29 C28 H281 C H sing 1.09 N N
30 C28 H282 C H sing 1.09 N N
31 C26 O27 C O doub 1.21 N N
32 C26 N25 C N sing 1.35 N N
33 N25 C9 N C sing 1.46 N N
34 N25 H25 N H sing 0.97 N N
35 C9 C7 C C sing 1.51 N N
36 C9 C10 C C sing 1.53 N N
37 C9 H9 C H sing 1.09 N N
38 C7 O8 C O doub 1.21 N N
39 C7 N6 C N sing 1.35 N N
40 N6 C4 N C sing 1.47 N N
41 N6 HN6 N H sing 0.97 N N
42 C4 C5 C C sing 1.53 N N
43 C4 B1 C B sing 1.57 N N
44 C4 H4 C H sing 1.09 N N
45 C5 H51 C H sing 1.09 N N
46 C5 H52 C H sing 1.09 N N
47 C5 H53 C H sing 1.09 N N
48 B1 O3 B O sing 1.42 N N
49 B1 O2 B O sing 1.42 N N
50 O3 HO3 O H sing 0.97 N N
51 O2 HO2 O H sing 0.97 N N
52 C10 C11 C C sing 1.53 N N
53 C10 H101 C H sing 1.09 N N
54 C10 H102 C H sing 1.09 N N
55 C11 C12 C C sing 1.53 N N
56 C11 H111 C H sing 1.09 N N
57 C11 H112 C H sing 1.09 N N
58 C12 C13 C C sing 1.53 N N
59 C12 H121 C H sing 1.09 N N
60 C12 H122 C H sing 1.09 N N
61 C13 N14 C N sing 1.46 N N
62 C13 H131 C H sing 1.09 N N
63 C13 H132 C H sing 1.09 N N
64 N14 C15 N C sing 1.35 N N
65 N14 H14 N H sing 0.97 N N
66 C15 O16 C O doub 1.22 N N
67 C15 O17 C O sing 1.35 N N
68 O17 C18 O C sing 1.45 N N
69 C18 C19 C C sing 1.51 N N
70 C18 H181 C H sing 1.09 N N
71 C18 H182 C H sing 1.09 N N
72 C19 C24 C C doub 1.38 N Y
73 C19 C20 C C sing 1.38 N Y
74 C24 C23 C C sing 1.38 N Y
75 C24 H24 C H sing 1.08 N N
76 C23 C22 C C doub 1.38 N Y
77 C23 H23 C H sing 1.08 N N
78 C22 C21 C C sing 1.38 N Y
79 C22 H22 C H sing 1.08 N N
80 C21 C20 C C doub 1.38 N Y
81 C21 H21 C H sing 1.08 N N
82 C20 H20 C H sing 1.08 N N



BO9 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
BO9 1z6f Open in New Window Bound ligand 1 1