Chemical Components in the PDB

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UPB : Summary

Code

UPB

One-letter code

X

Molecule name

3-[5-[(~{Z})-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[(~{Z})-[5-[(~{Z})-[(4~{R})-3-ethyl-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-2-ylidene]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 3-[5-[(~{Z})-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[(~{Z})-[5-[(~{Z})-[(3~{Z},4~{R})-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-2-ylidene]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid

Formula

C33 H36 N4 O6

Formal charge

0

Molecular weight

584.662 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CC=C1[CH](C)C(=O)NC1=CC2=NC(=Cc3[nH]c(C=C4NC(=O)C(=C4C)C=C)c(C)c3CCC(O)=O)C(=C2C)CCC(O)=O
SMILES OpenEye OEToolkits 2.0.7 CC=C1C(C(=O)NC1=CC2=NC(=Cc3c(c(c([nH]3)C=C4C(=C(C(=O)N4)C=C)C)C)CCC(=O)O)C(=C2C)CCC(=O)O)C
Canonical SMILES CACTVS 3.385 C\C=C/1[C@@H](C)C(=O)NC/1=C/C2=N\C(=C/c3[nH]c(\C=C4/NC(=O)C(=C4C)C=C)c(C)c3CCC(O)=O)C(=C2C)CCC(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 C/C=C\1/[C@H](C(=O)N/C1=C\C2=N/C(=C\c3c(c(c([nH]3)/C=C\4/C(=C(C(=O)N4)C=C)C)C)CCC(=O)O)/C(=C2C)CCC(=O)O)C

IUPAC InChI

InChI=1S/C33H36N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-15,19,34H,2,9-12H2,1,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b20-7-,26-13-,27-14-,29-15-/t19-/m1/s1

IUPAC InChI key

SNHIGJASYQUMKZ-NSNBCYBJSA-N
UPB

wwPDB Information

Atom count

79 (43 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-03-16

Last modified at

2021-08-20

Status

Released

Obsoleted

Not Assigned



UPB : Atoms of Molecule

Total Number of Atoms: 79
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CHA C C1 N N N 0 2.261 -0.157 -0.595
2 NA N N1 N Y N 0 0.142 -1.409 -0.329
3 C1A C C2 N Y N 0 1.515 -1.328 -0.409
4 C2A C C3 N Y N 0 2.032 -2.618 -0.271
5 C3A C C4 N Y N 0 0.966 -3.482 -0.108
6 C4A C C5 N Y N 0 -0.204 -2.724 -0.145
7 CMA C C6 N N N 0 1.052 -4.975 0.077
8 CAA C C7 N N N 0 3.49 -2.999 -0.297
9 CBA C C8 N N N 0 4.056 -2.947 1.124
10 CGA C C9 N N N 0 5.514 -3.328 1.098
11 O1A O O1 N N N 0 6.221 -3.352 2.238
12 O2A O O2 N N N 0 6.045 -3.612 0.051
13 CHB C C10 N N N 0 -1.515 -3.222 -0.01
14 NB N N2 N N N 0 -2.483 -1.385 -1.334
15 C1B C C11 N N N 0 -2.581 -2.514 -0.532
16 C2B C C12 N N N 0 -3.94 -2.821 -0.337
17 C3B C C13 N N N 0 -4.682 -1.875 -1.023
18 C4B C C14 N N N 0 -3.72 -0.962 -1.656
19 CMB C C15 N N N 0 -4.487 -3.969 0.471
20 OB O O3 N N N 0 -3.993 0.006 -2.343
21 CAB C C16 N N N 0 -6.15 -1.799 -1.103
22 CBB C C17 N N N 0 -6.728 -0.856 -1.842
23 NC N N3 N N N 0 -2.015 1.133 1.223
24 C1C C C18 N N N 0 -3.147 0.642 1.748
25 C2C C C19 R N N 0 -4.141 1.771 1.897
26 C3C C C20 N N N 0 -3.41 2.993 1.375
27 C4C C C21 N N N 0 -2.085 2.493 0.975
28 CMC C C22 N N N 0 -5.391 1.495 1.058
29 OC O O4 N N N 0 -3.341 -0.515 2.055
30 CAC C C23 N N N 0 -3.866 4.242 1.295
31 CBC C C24 N N N 0 -2.985 5.332 0.743
32 CHD C C25 N N N 0 -1.085 3.249 0.446
33 ND N N4 N N N 0 0.405 1.31 0.009
34 C1D C C26 N N N 0 0.162 2.616 0.018
35 C2D C C27 N N N 0 1.313 3.294 -0.456
36 C3D C C28 N N N 0 2.241 2.347 -0.745
37 C4D C C29 N N N 0 1.652 1.091 -0.445
38 CMD C C30 N N N 0 1.475 4.785 -0.611
39 CAD C C31 N N N 0 3.63 2.583 -1.282
40 CBD C C32 N N N 0 4.625 2.624 -0.12
41 CGD C C33 N N N 0 6.013 2.86 -0.656
42 O1D O O5 N N N 0 7.055 2.934 0.187
43 O2D O O6 N N N 0 6.189 2.984 -1.845
44 H1 H H1 N N N 0 3.309 -0.219 -0.851
45 H3 H H3 N N N 0 -0.475 -0.663 -0.389
46 H4 H H4 N N N 0 1.124 -5.206 1.14
47 H5 H H5 N N N 0 0.16 -5.445 -0.337
48 H6 H H6 N N N 0 1.935 -5.354 -0.438
49 H7 H H7 N N N 0 3.595 -4.009 -0.693
50 H8 H H8 N N N 0 4.037 -2.301 -0.932
51 H9 H H9 N N N 0 3.951 -1.937 1.52
52 H10 H H10 N N N 0 3.509 -3.644 1.758
53 H11 H H11 N N N 0 7.153 -3.602 2.172
54 H12 H H12 N N N 0 -1.688 -4.158 0.501
55 H14 H H14 N N N 0 -4.634 -3.65 1.503
56 H15 H H15 N N N 0 -5.441 -4.287 0.05
57 H16 H H16 N N N 0 -3.783 -4.8 0.444
58 H17 H H17 N N N 0 -6.758 -2.509 -0.562
59 H18 H H18 N N N 0 -7.802 -0.742 -1.828
60 H19 H H19 N N N 0 -6.123 -0.204 -2.454
61 H20 H H20 N N N 0 -1.23 0.593 1.039
62 H25 H H25 N N N 0 -5.102 1.319 0.022
63 H21 H H21 N N N 0 -4.409 1.907 2.944
64 H23 H H23 N N N 0 -5.903 0.615 1.448
65 H24 H H24 N N N 0 -6.059 2.355 1.107
66 H26 H H26 N N N 0 -4.868 4.473 1.626
67 H28 H H28 N N N 0 -3.526 6.279 0.756
68 H29 H H29 N N N 0 -2.087 5.419 1.355
69 H30 H H30 N N N 0 -2.704 5.089 -0.282
70 H31 H H31 N N N 0 -1.213 4.316 0.342
71 H33 H H33 N N N 0 0.558 5.284 -0.298
72 H34 H H34 N N N 0 2.305 5.126 0.008
73 H35 H H35 N N N 0 1.679 5.021 -1.655
74 H36 H H36 N N N 0 3.898 1.776 -1.962
75 H37 H H37 N N N 0 3.656 3.533 -1.816
76 H38 H H38 N N N 0 4.356 3.432 0.561
77 H39 H H39 N N N 0 4.598 1.674 0.414
78 H40 H H40 N N N 0 7.926 3.087 -0.204
79 H2 H H2 N N N 0 -1.654 -0.965 -1.614



UPB : 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 O2D CGD O C doub 1.21 N N
2 CGD O1D C O sing 1.34 N N
3 CGD CBD C C sing 1.51 N N
4 O2A CGA O C doub 1.21 N N
5 CBD CAD C C sing 1.53 N N
6 O1A CGA O C sing 1.34 N N
7 CGA CBA C C sing 1.51 N N
8 CAD C3D C C sing 1.51 N N
9 CBA CAA C C sing 1.53 N N
10 CMD C2D C C sing 1.51 N N
11 C3D C2D C C doub 1.36 N N
12 C3D C4D C C sing 1.42 N N
13 C2D C1D C C sing 1.42 N N
14 CAA C2A C C sing 1.51 N N
15 C4D CHA C C doub 1.4 Z N
16 C4D ND C N sing 1.35 N N
17 CHA C1A C C sing 1.4 N N
18 C1D ND C N doub 1.33 N N
19 C1D CHD C C sing 1.46 N N
20 CHD C4C C C doub 1.36 Z N
21 C1A C2A C C doub 1.4 N Y
22 C1A NA C N sing 1.38 N Y
23 C2A C3A C C sing 1.38 N Y
24 NC C4C N C sing 1.38 N N
25 NC C1C N C sing 1.34 N N
26 C4C C3C C C sing 1.47 N N
27 CMC C2C C C sing 1.53 N N
28 OC C1C O C doub 1.21 N N
29 C1C C2C C C sing 1.51 N N
30 C3A CMA C C sing 1.51 N N
31 C3A C4A C C doub 1.39 N Y
32 NA C4A N C sing 1.37 N Y
33 C3C CAC C C doub 1.33 Z N
34 C3C C2C C C sing 1.52 N N
35 CAC CBC C C sing 1.51 N N
36 C4A CHB C C sing 1.41 N N
37 CHB C1B C C doub 1.38 Z N
38 C1B NB C N sing 1.39 N N
39 C1B C2B C C sing 1.41 N N
40 NB C4B N C sing 1.35 N N
41 C2B CMB C C sing 1.51 N N
42 C2B C3B C C doub 1.38 N N
43 C4B C3B C C sing 1.47 N N
44 C4B OB C O doub 1.22 N N
45 C3B CAB C C sing 1.47 N N
46 CBB CAB C C doub 1.33 N N
47 CHA H1 C H sing 1.08 N N
48 NA H3 N H sing 0.97 N N
49 CMA H4 C H sing 1.09 N N
50 CMA H5 C H sing 1.09 N N
51 CMA H6 C H sing 1.09 N N
52 CAA H7 C H sing 1.09 N N
53 CAA H8 C H sing 1.09 N N
54 CBA H9 C H sing 1.09 N N
55 CBA H10 C H sing 1.09 N N
56 O1A H11 O H sing 0.97 N N
57 CHB H12 C H sing 1.08 N N
58 CMB H14 C H sing 1.09 N N
59 CMB H15 C H sing 1.09 N N
60 CMB H16 C H sing 1.09 N N
61 CAB H17 C H sing 1.08 N N
62 CBB H18 C H sing 1.08 N N
63 CBB H19 C H sing 1.08 N N
64 NC H20 N H sing 0.97 N N
65 C2C H21 C H sing 1.09 N N
66 CMC H23 C H sing 1.09 N N
67 CMC H24 C H sing 1.09 N N
68 CMC H25 C H sing 1.09 N N
69 CAC H26 C H sing 1.08 N N
70 CBC H28 C H sing 1.09 N N
71 CBC H29 C H sing 1.09 N N
72 CBC H30 C H sing 1.09 N N
73 CHD H31 C H sing 1.08 N N
74 CMD H33 C H sing 1.09 N N
75 CMD H34 C H sing 1.09 N N
76 CMD H35 C H sing 1.09 N N
77 CAD H36 C H sing 1.09 N N
78 CAD H37 C H sing 1.09 N N
79 CBD H38 C H sing 1.09 N N
80 CBD H39 C H sing 1.09 N N
81 O1D H40 O H sing 0.97 N N
82 NB H2 N H sing 0.97 N N



UPB : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
UPB 7e2u Open in New Window Bound ligand 1 1