Chemical Components in the PDB

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7J8 : Summary

Code

7J8

One-letter code

X

Molecule name

3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-1~{H}-pyrrol-3-yl]propanoic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-1~{H}-pyrrol-3-yl]propanoic acid

Formula

C40 H46 N4 O16

Formal charge

0

Molecular weight

838.81 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Cc1[nH]c(Cc2[nH]c(Cc3[nH]c(Cc4[nH]cc(CCC(O)=O)c4CC(O)=O)c(CCC(O)=O)c3CC(O)=O)c(CCC(O)=O)c2CC(O)=O)c(CCC(O)=O)c1CC(O)=O
SMILES OpenEye OEToolkits 2.0.6 Cc1c(c(c([nH]1)Cc2c(c(c([nH]2)Cc3c(c(c([nH]3)Cc4c(c(c[nH]4)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
Canonical SMILES CACTVS 3.385 Cc1[nH]c(Cc2[nH]c(Cc3[nH]c(Cc4[nH]cc(CCC(O)=O)c4CC(O)=O)c(CCC(O)=O)c3CC(O)=O)c(CCC(O)=O)c2CC(O)=O)c(CCC(O)=O)c1CC(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.6 Cc1c(c(c([nH]1)Cc2c(c(c([nH]2)Cc3c(c(c([nH]3)Cc4c(c(c[nH]4)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O

IUPAC InChI

InChI=1S/C40H46N4O16/c1-18-23(10-37(53)54)20(3-7-34(47)48)28(42-18)15-31-26(13-40(59)60)22(5-9-36(51)52)30(44-31)16-32-25(12-39(57)58)21(4-8-35(49)50)29(43-32)14-27-24(11-38(55)56)19(17-41-27)2-6-33(45)46/h17,41-44H,2-16H2,1H3,(H,45,46)(H,47,48)(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)

IUPAC InChI key

VHZWMEJYGVBAFI-UHFFFAOYSA-N
7J8

wwPDB Information

Atom count

106 (60 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-11-01

Last modified at

2017-11-10

Status

Released

Obsoleted

Not Assigned



7J8 : Atoms of Molecule

Total Number of Atoms: 106
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O15 O O1 N N N 0 -4.568 -3.326 -2.458
2 C39 C C1 N N N 0 -4.097 -2.248 -2.733
3 O14 O O2 N N N 0 -3.128 -2.155 -3.657
4 C38 C C2 N N N 0 -4.602 -1.007 -2.043
5 C37 C C3 N N N 0 -5.701 -1.388 -1.049
6 C5 C C4 N Y N 0 -6.206 -0.147 -0.359
7 C2 C C5 N Y N 0 -7.267 0.674 -0.79
8 C3 C C6 N N N 0 -8.105 0.472 -2.026
9 C4 C C7 N N N 0 -9.299 -0.384 -1.689
10 O1 O O3 N N N 0 -9.453 -0.789 -0.561
11 O O O4 N N N 0 -10.191 -0.697 -2.642
12 C6 C C8 N Y N 0 -5.728 0.379 0.787
13 N3 N N1 N Y N 0 -6.453 1.497 1.077
14 C1 C C9 N Y N 0 -7.394 1.673 0.107
15 C C C10 N N N 0 -8.404 2.79 0.047
16 C7 C C11 N N N 0 -4.591 -0.174 1.607
17 C8 C C12 N Y N 0 -3.283 0.334 1.058
18 N2 N N2 N Y N 0 -2.487 -0.315 0.161
19 C13 C C13 N Y N 0 -1.393 0.459 -0.093
20 C12 C C14 N Y N 0 -1.497 1.588 0.636
21 C34 C C15 N N N 0 -0.509 2.726 0.663
22 C35 C C16 N N N 0 -0.878 3.748 -0.414
23 C36 C C17 N N N 0 0.109 4.886 -0.387
24 O13 O O5 N N N 0 1.015 4.88 0.412
25 O12 O O6 N N N 0 -0.018 5.905 -1.251
26 C9 C C18 N Y N 0 -2.701 1.511 1.364
27 C10 C C19 N N N 0 -3.237 2.552 2.312
28 C11 C C20 N N N 0 -2.723 2.278 3.702
29 O3 O O7 N N N 0 -1.996 1.334 3.902
30 O2 O O8 N N N 0 -3.074 3.082 4.718
31 C14 C C21 N N N 0 -0.263 0.111 -1.028
32 C15 C C22 N Y N 0 0.859 -0.522 -0.246
33 N1 N N3 N Y N 0 1.946 0.126 0.26
34 C20 C C23 N Y N 0 2.736 -0.78 0.903
35 C19 C C24 N Y N 0 2.154 -1.992 0.804
36 C31 C C25 N N N 0 2.682 -3.284 1.372
37 C32 C C26 N N N 0 2.144 -3.476 2.791
38 C33 C C27 N N N 0 2.672 -4.768 3.358
39 O11 O O9 N N N 0 3.404 -5.465 2.695
40 O10 O O10 N N N 0 2.329 -5.146 4.6
41 C16 C C28 N Y N 0 0.957 -1.828 0.078
42 C17 C C29 N N N 0 -0.029 -2.911 -0.274
43 C18 C C30 N N N 0 0.347 -3.521 -1.6
44 O5 O O11 N N N 0 1.315 -3.116 -2.198
45 O4 O O12 N N N 0 -0.396 -4.513 -2.117
46 C21 C C31 N N N 0 4.037 -0.479 1.602
47 C22 C C32 N Y N 0 5.185 -0.738 0.661
48 N N N4 N Y N 0 5.905 -1.893 0.577
49 C27 C C33 N Y N 0 6.856 -1.747 -0.388
50 C26 C C34 N Y N 0 6.74 -0.51 -0.911
51 C28 C C35 N N N 0 7.59 0.078 -2.007
52 C29 C C36 N N N 0 8.732 0.887 -1.389
53 C30 C C37 N N N 0 9.582 1.476 -2.485
54 O9 O O13 N N N 0 9.303 1.269 -3.643
55 O8 O O14 N N N 0 10.649 2.229 -2.176
56 C23 C C38 N Y N 0 5.674 0.13 -0.248
57 C24 C C39 N N N 0 5.174 1.528 -0.505
58 C25 C C40 N N N 0 5.916 2.497 0.379
59 O7 O O15 N N N 0 6.764 2.093 1.139
60 O6 O O16 N N N 0 5.636 3.808 0.321
61 H45 H H1 N N N 0 -2.84 -2.978 -4.076
62 H43 H H2 N N N 0 -3.78 -0.528 -1.511
63 H44 H H3 N N N 0 -5.005 -0.318 -2.785
64 H42 H H4 N N N 0 -6.522 -1.867 -1.582
65 H41 H H5 N N N 0 -5.297 -2.077 -0.308
66 H8 H H6 N N N 0 -8.445 1.439 -2.396
67 H7 H H7 N N N 0 -7.509 -0.022 -2.793
68 H9 H H8 N N N 0 -10.94 -1.248 -2.378
69 H3 H H9 N N N 0 -6.322 2.072 1.848
70 H6 H H10 N N N 0 -7.984 3.63 -0.507
71 H5 H H11 N N N 0 -9.306 2.439 -0.454
72 H4 H H12 N N N 0 -8.651 3.111 1.059
73 H11 H H13 N N N 0 -4.7 0.148 2.643
74 H10 H H14 N N N 0 -4.606 -1.263 1.561
75 H2 H H15 N N N 0 -2.668 -1.184 -0.23
76 H36 H H16 N N N 0 -0.534 3.205 1.642
77 H37 H H17 N N N 0 0.493 2.342 0.471
78 H38 H H18 N N N 0 -0.854 3.269 -1.393
79 H39 H H19 N N N 0 -1.88 4.132 -0.223
80 H40 H H20 N N N 0 0.639 6.612 -1.195
81 H12 H H21 N N N 0 -2.908 3.54 1.992
82 H13 H H22 N N N 0 -4.327 2.515 2.314
83 H14 H H23 N N N 0 -2.719 2.866 5.591
84 H16 H H24 N N N 0 -0.619 -0.589 -1.784
85 H15 H H25 N N N 0 0.099 1.017 -1.513
86 H1 H H26 N N N 0 2.127 1.075 0.176
87 H33 H H30 N N N 0 1.055 -3.509 2.765
88 H31 H H27 N N N 0 2.359 -4.115 0.745
89 H32 H H28 N N N 0 3.771 -3.251 1.398
90 H34 H H29 N N N 0 2.467 -2.645 3.417
91 H35 H H31 N N N 0 2.693 -5.983 4.92
92 H18 H H32 N N N 0 -0.013 -3.682 0.498
93 H20 H H36 N N N 0 4.134 -1.118 2.479
94 H17 H H33 N N N 0 -1.029 -2.484 -0.34
95 H19 H H34 N N N 0 -0.116 -4.872 -2.97
96 H21 H H35 N N N 0 4.049 0.566 1.911
97 H H H37 N N N 0 5.763 -2.688 1.116
98 H25 H H38 N N N 0 7.579 -2.494 -0.682
99 H27 H H39 N N N 0 8.003 -0.725 -2.618
100 H26 H H40 N N N 0 6.978 0.731 -2.631
101 H29 H H41 N N N 0 8.319 1.691 -0.779
102 H28 H H42 N N N 0 9.344 0.235 -0.766
103 H30 H H43 N N N 0 11.164 2.585 -2.914
104 H23 H H44 N N N 0 5.342 1.787 -1.55
105 H22 H H45 N N N 0 4.108 1.579 -0.285
106 H24 H H46 N N N 0 6.138 4.391 0.907



7J8 : Chemical Bonds

Total Number of Bonds: 109
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C C1 C C sing 1.51 N N
2 O3 C11 O C doub 1.21 N N
3 O C4 O C sing 1.34 N N
4 C1 N3 C N sing 1.36 N Y
5 C1 C2 C C doub 1.35 N Y
6 N3 C6 N C sing 1.36 N Y
7 C11 O2 C O sing 1.34 N N
8 C11 C10 C C sing 1.51 N N
9 C4 O1 C O doub 1.21 N N
10 C4 C3 C C sing 1.51 N N
11 C2 C3 C C sing 1.51 N N
12 C2 C5 C C sing 1.41 N Y
13 C6 C7 C C sing 1.51 N N
14 C6 C5 C C doub 1.35 N Y
15 C7 C8 C C sing 1.51 N N
16 C10 C9 C C sing 1.51 N N
17 C5 C37 C C sing 1.51 N N
18 C8 C9 C C doub 1.35 N Y
19 C8 N2 C N sing 1.36 N Y
20 C9 C12 C C sing 1.41 N Y
21 C37 C38 C C sing 1.53 N N
22 N2 C13 N C sing 1.36 N Y
23 C12 C34 C C sing 1.51 N N
24 C12 C13 C C doub 1.35 N Y
25 C38 C39 C C sing 1.51 N N
26 O13 C36 O C doub 1.21 N N
27 C34 C35 C C sing 1.53 N N
28 C35 C36 C C sing 1.51 N N
29 C36 O12 C O sing 1.34 N N
30 C13 C14 C C sing 1.51 N N
31 O15 C39 O C doub 1.21 N N
32 C39 O14 C O sing 1.34 N N
33 C14 C15 C C sing 1.51 N N
34 N1 C15 N C sing 1.36 N Y
35 N1 C20 N C sing 1.36 N Y
36 C15 C16 C C doub 1.35 N Y
37 C20 C21 C C sing 1.51 N N
38 C20 C19 C C doub 1.35 N Y
39 C21 C22 C C sing 1.51 N N
40 N C22 N C sing 1.36 N Y
41 N C27 N C sing 1.36 N Y
42 C16 C19 C C sing 1.41 N Y
43 C16 C17 C C sing 1.51 N N
44 C19 C31 C C sing 1.51 N N
45 C17 C18 C C sing 1.51 N N
46 C22 C23 C C doub 1.35 N Y
47 C31 C32 C C sing 1.53 N N
48 C27 C26 C C doub 1.35 N Y
49 C18 O4 C O sing 1.34 N N
50 C18 O5 C O doub 1.21 N N
51 O11 C33 O C doub 1.21 N N
52 C23 C26 C C sing 1.41 N Y
53 C23 C24 C C sing 1.51 N N
54 C26 C28 C C sing 1.51 N N
55 C32 C33 C C sing 1.51 N N
56 C33 O10 C O sing 1.34 N N
57 O8 C30 O C sing 1.34 N N
58 C24 C25 C C sing 1.51 N N
59 O9 C30 O C doub 1.21 N N
60 C30 C29 C C sing 1.51 N N
61 C28 C29 C C sing 1.53 N N
62 O6 C25 O C sing 1.34 N N
63 C25 O7 C O doub 1.21 N N
64 O14 H45 O H sing 0.97 N N
65 C38 H43 C H sing 1.09 N N
66 C38 H44 C H sing 1.09 N N
67 C37 H42 C H sing 1.09 N N
68 C37 H41 C H sing 1.09 N N
69 C3 H8 C H sing 1.09 N N
70 C3 H7 C H sing 1.09 N N
71 O H9 O H sing 0.97 N N
72 N3 H3 N H sing 0.97 N N
73 C H6 C H sing 1.09 N N
74 C H5 C H sing 1.09 N N
75 C H4 C H sing 1.09 N N
76 C7 H11 C H sing 1.09 N N
77 C7 H10 C H sing 1.09 N N
78 N2 H2 N H sing 0.97 N N
79 C34 H36 C H sing 1.09 N N
80 C34 H37 C H sing 1.09 N N
81 C35 H38 C H sing 1.09 N N
82 C35 H39 C H sing 1.09 N N
83 O12 H40 O H sing 0.97 N N
84 C10 H12 C H sing 1.09 N N
85 C10 H13 C H sing 1.09 N N
86 O2 H14 O H sing 0.97 N N
87 C14 H16 C H sing 1.09 N N
88 C14 H15 C H sing 1.09 N N
89 N1 H1 N H sing 0.97 N N
90 C31 H31 C H sing 1.09 N N
91 C31 H32 C H sing 1.09 N N
92 C32 H34 C H sing 1.09 N N
93 C32 H33 C H sing 1.09 N N
94 O10 H35 O H sing 0.97 N N
95 C17 H18 C H sing 1.09 N N
96 C17 H17 C H sing 1.09 N N
97 O4 H19 O H sing 0.97 N N
98 C21 H21 C H sing 1.09 N N
99 C21 H20 C H sing 1.09 N N
100 N H N H sing 0.97 N N
101 C27 H25 C H sing 1.08 N N
102 C28 H27 C H sing 1.09 N N
103 C28 H26 C H sing 1.09 N N
104 C29 H29 C H sing 1.09 N N
105 C29 H28 C H sing 1.09 N N
106 O8 H30 O H sing 0.97 N N
107 C24 H23 C H sing 1.09 N N
108 C24 H22 C H sing 1.09 N N
109 O6 H24 O H sing 0.97 N N



7J8 : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
7J8 5m6r Open in New Window Bound ligand 2 1
7J8 7aak Open in New Window Bound ligand 2 1
7J8 7ccz Open in New Window Bound ligand 2 1
7J8 7cd0 Open in New Window Bound ligand 2 1