Chemical Components in the PDB

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ZXY : Summary

Code

ZXY

One-letter code

X

Molecule name

N-(3-{[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-1-benzopyran-3-yl]oxy}propyl)-1-[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]-L-prolinamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-(3-{[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-1-benzopyran-3-yl]oxy}propyl)-1-[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]-L-prolinamide
OpenEye OEToolkits 2.0.7 (2~{S})-~{N}-[3-[2-[3,4-bis(oxidanyl)phenyl]-5,7-bis(oxidanyl)-4-oxidanylidene-chromen-3-yl]oxypropyl]-1-[(~{E})-3-[3,4-bis(oxidanyl)phenyl]prop-2-enoyl]pyrrolidine-2-carboxamide

Formula

C32 H30 N2 O11

Formal charge

0

Molecular weight

618.587 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N4(C(C(=O)NCCCOC=1C(c3c(OC=1c2ccc(c(c2)O)O)cc(cc3O)O)=O)CCC4)C(=O)[C@H]=[C@H]c5ccc(c(c5)O)O
SMILES CACTVS 3.385 Oc1cc(O)c2C(=O)C(=C(Oc2c1)c3ccc(O)c(O)c3)OCCCNC(=O)[CH]4CCCN4C(=O)C=Cc5ccc(O)c(O)c5
SMILES OpenEye OEToolkits 2.0.7 c1cc(c(cc1C=CC(=O)N2CCCC2C(=O)NCCCOC3=C(Oc4cc(cc(c4C3=O)O)O)c5ccc(c(c5)O)O)O)O
Canonical SMILES CACTVS 3.385 Oc1cc(O)c2C(=O)C(=C(Oc2c1)c3ccc(O)c(O)c3)OCCCNC(=O)[C@@H]4CCCN4C(=O)/C=C/c5ccc(O)c(O)c5
Canonical SMILES OpenEye OEToolkits 2.0.7 c1cc(c(cc1/C=C/C(=O)N2CCC[C@H]2C(=O)NCCCOC3=C(Oc4cc(cc(c4C3=O)O)O)c5ccc(c(c5)O)O)O)O

IUPAC InChI

InChI=1S/C32H30N2O11/c35-19-15-25(40)28-26(16-19)45-30(18-6-8-22(37)24(39)14-18)31(29(28)42)44-12-2-10-33-32(43)20-3-1-11-34(20)27(41)9-5-17-4-7-21(36)23(38)13-17/h4-9,13-16,20,35-40H,1-3,10-12H2,(H,33,43)/b9-5+/t20-/m0/s1

IUPAC InChI key

MYJPTGWVMBCTRI-MRSBXDGLSA-N
ZXY

wwPDB Information

Atom count

75 (45 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-03-25

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



ZXY : Atoms of Molecule

Total Number of Atoms: 75
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N1 N N N 0 4.716 0.153 2.194
2 CA C C1 S N N 0 3.395 -0.139 2.771
3 CB C C2 N N N 0 3.333 0.553 4.148
4 CG C C3 N N N 0 4.407 1.666 4.027
5 CD C C4 N N N 0 5.481 0.968 3.156
6 C C C5 N N N 0 2.313 0.405 1.874
7 O O O1 N N N 0 2.578 1.255 1.051
8 N1 N N2 N N N 0 1.05 -0.052 1.988
9 C2 C C6 N N N 0 -0.002 0.477 1.117
10 C3 C C7 N N N 0 -1.331 -0.205 1.449
11 C4 C C8 N N N 0 -2.451 0.434 0.627
12 O5 O O2 N N N 0 -3.707 -0.123 1.02
13 C6 C C9 N N N 0 -4.803 0.26 0.309
14 C7 C C10 N N N 0 -5.481 -0.646 -0.45
15 O6 O O3 N N N 0 -6.57 -0.317 -1.164
16 C9 C C11 N Y N 0 -7.07 0.936 -1.181
17 C10 C C12 N Y N 0 -6.446 1.949 -0.432
18 C11 C C13 N N N 0 -5.252 1.605 0.356
19 C13 C C15 N Y N 0 -8.698 2.532 -1.938
20 C12 C C14 N Y N 0 -8.197 1.24 -1.931
21 C14 C C16 N Y N 0 -8.082 3.536 -1.197
22 C15 C C17 N Y N 0 -6.959 3.253 -0.444
23 O16 O O4 N N N 0 -4.674 2.444 1.029
24 O17 O O5 N N N 0 -6.356 4.231 0.279
25 O18 O O6 N N N 0 -9.8 2.821 -2.675
26 C19 C C18 N Y N 0 -5.001 -2.04 -0.488
27 C23 C C22 N Y N 0 -4.41 -4.001 -1.747
28 C20 C C19 N Y N 0 -4.686 -2.706 0.7
29 C21 C C20 N Y N 0 -4.238 -4.012 0.658
30 C22 C C21 N Y N 0 -4.099 -4.662 -0.568
31 C24 C C23 N Y N 0 -4.864 -2.7 -1.712
32 O25 O O7 N N N 0 -3.656 -5.946 -0.607
33 O26 O O8 N N N 0 -3.931 -4.663 1.812
34 C27 C C24 N N N 0 5.156 -0.26 0.989
35 C28 C C25 N N N 0 6.498 0.105 0.537
36 C29 C C26 N N N 0 6.939 -0.309 -0.67
37 O30 O O9 N N N 0 4.437 -0.936 0.278
38 C31 C C27 N Y N 0 8.288 0.057 -1.125
39 C32 C C28 N Y N 0 9.117 0.835 -0.308
40 C33 C C29 N Y N 0 10.381 1.176 -0.737
41 C34 C C30 N Y N 0 10.836 0.751 -1.977
42 C35 C C31 N Y N 0 10.016 -0.024 -2.797
43 C36 C C32 N Y N 0 8.75 -0.376 -2.373
44 O37 O O10 N N N 0 12.083 1.092 -2.395
45 O38 O O11 N N N 0 10.465 -0.438 -4.012
46 HA H H1 N N N 0 3.272 -1.216 2.888
47 HB3 H H2 N N N 0 2.347 0.985 4.319
48 HB2 H H3 N N N 0 3.588 -0.148 4.944
49 HG3 H H4 N N N 0 4.004 2.544 3.523
50 HG2 H H5 N N N 0 4.808 1.93 5.006
51 HD3 H H6 N N N 0 6.115 0.331 3.773
52 HD2 H H7 N N N 0 6.083 1.709 2.63
53 HN1 H H8 N N N 0 0.838 -0.732 2.647
54 H21 H H9 N N N 0 -0.096 1.552 1.272
55 H2 H H10 N N N 0 0.256 0.282 0.076
56 H3 H H11 N N N 0 -1.264 -1.266 1.211
57 H31 H H12 N N N 0 -1.545 -0.084 2.511
58 H4 H H13 N N N 0 -2.461 1.51 0.799
59 H41 H H14 N N N 0 -2.283 0.237 -0.432
60 H12 H H15 N N N 0 -8.683 0.47 -2.51
61 H14 H H16 N N N 0 -8.483 4.539 -1.212
62 HO17 H H17 N N N 0 -6.695 4.319 1.18
63 HO18 H H18 N N N 0 -10.634 2.71 -2.197
64 H20 H H19 N N N 0 -4.794 -2.201 1.648
65 H23 H H20 N N N 0 -4.301 -4.509 -2.694
66 H24 H H21 N N N 0 -5.11 -2.189 -2.632
67 HO25 H H22 N N N 0 -4.361 -6.607 -0.56
68 HO26 H H23 N N N 0 -4.675 -5.14 2.204
69 H28 H H24 N N N 0 7.136 0.705 1.168
70 H29 H H25 N N N 0 6.301 -0.909 -1.301
71 H32 H H26 N N N 0 8.766 1.167 0.658
72 H33 H H27 N N N 0 11.02 1.777 -0.106
73 H36 H H28 N N N 0 8.114 -0.976 -3.007
74 HO37 H H29 N N N 0 12.768 0.457 -2.145
75 HO38 H H30 N N N 0 10.92 -1.291 -3.994



ZXY : Chemical Bonds

Total Number of Bonds: 79
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O37 C34 O C sing 1.36 N N
2 O18 C13 O C sing 1.36 N N
3 C34 C33 C C doub 1.39 N Y
4 C34 C35 C C sing 1.39 N Y
5 C13 C12 C C doub 1.39 N Y
6 C13 C14 C C sing 1.39 N Y
7 O38 C35 O C sing 1.36 N N
8 C12 C9 C C sing 1.39 N Y
9 O26 C21 O C sing 1.36 N N
10 C33 C32 C C sing 1.38 N Y
11 C35 C36 C C doub 1.38 N Y
12 C21 C20 C C doub 1.38 N Y
13 C21 C22 C C sing 1.39 N Y
14 C14 C15 C C doub 1.38 N Y
15 C20 C19 C C sing 1.4 N Y
16 C9 O6 C O sing 1.35 N N
17 C9 C10 C C doub 1.41 N Y
18 O6 C7 O C sing 1.34 N N
19 C32 C31 C C doub 1.4 N Y
20 O25 C22 O C sing 1.36 N N
21 C36 C31 C C sing 1.4 N Y
22 C22 C23 C C doub 1.39 N Y
23 C19 C7 C C sing 1.47 N N
24 C19 C24 C C doub 1.4 N Y
25 C15 C10 C C sing 1.4 N Y
26 C15 O17 C O sing 1.36 N N
27 C10 C11 C C sing 1.47 N N
28 C7 C6 C C doub 1.36 N N
29 C31 C29 C C sing 1.47 N N
30 C23 C24 C C sing 1.38 N Y
31 C6 C11 C C sing 1.42 N N
32 C6 O5 C O sing 1.36 N N
33 C11 O16 C O doub 1.22 N N
34 C29 C28 C C doub 1.35 E N
35 C28 C27 C C sing 1.46 N N
36 O5 C4 O C sing 1.43 N N
37 C4 C3 C C sing 1.53 N N
38 C27 O30 C O doub 1.22 N N
39 C27 N C N sing 1.35 N N
40 CD N C N sing 1.47 N N
41 CD CG C C sing 1.55 N N
42 N CA N C sing 1.47 N N
43 C3 C2 C C sing 1.53 N N
44 CG CB C C sing 1.55 N N
45 N1 C2 N C sing 1.46 N N
46 N1 C N C sing 1.35 N N
47 CA C C C sing 1.51 N N
48 CA CB C C sing 1.54 N N
49 C O C O doub 1.21 N N
50 CA HA C H sing 1.09 N N
51 CB HB3 C H sing 1.09 N N
52 CB HB2 C H sing 1.09 N N
53 CG HG3 C H sing 1.09 N N
54 CG HG2 C H sing 1.09 N N
55 CD HD3 C H sing 1.09 N N
56 CD HD2 C H sing 1.09 N N
57 N1 HN1 N H sing 0.97 N N
58 C2 H21 C H sing 1.09 N N
59 C2 H2 C H sing 1.09 N N
60 C3 H3 C H sing 1.09 N N
61 C3 H31 C H sing 1.09 N N
62 C4 H4 C H sing 1.09 N N
63 C4 H41 C H sing 1.09 N N
64 C12 H12 C H sing 1.08 N N
65 C14 H14 C H sing 1.08 N N
66 O17 HO17 O H sing 0.97 N N
67 O18 HO18 O H sing 0.97 N N
68 C20 H20 C H sing 1.08 N N
69 C23 H23 C H sing 1.08 N N
70 C24 H24 C H sing 1.08 N N
71 O25 HO25 O H sing 0.97 N N
72 O26 HO26 O H sing 0.97 N N
73 C28 H28 C H sing 1.08 N N
74 C29 H29 C H sing 1.08 N N
75 C32 H32 C H sing 1.08 N N
76 C33 H33 C H sing 1.08 N N
77 C36 H36 C H sing 1.08 N N
78 O37 HO37 O H sing 0.97 N N
79 O38 HO38 O H sing 0.97 N N



ZXY : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
ZXY 6ocn Open in New Window Bound ligand 1 1