Chemical Components in the PDB

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Z90 : Summary

Code

Z90

One-letter code

X

Molecule name

4-({(4-carboxybutyl)[2-(2-{[4-(2-phenylethyl)benzyl]oxy}phenyl)ethyl]amino}methyl)benzoic acid

Synonyms

4-((4-carboxybutyl)(2-((4-phenethylbenzol)oxy) phenethyl) amino)methyl(benzoic) acid)

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.6.1 4-[[(5-hydroxy-5-oxo-pentyl)-[2-[2-[(4-phenethylphenyl)methoxy]phenyl]ethyl]amino]methyl]benzoic acid

Formula

C36 H39 N O5

Formal charge

0

Molecular weight

565.699 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.352 OC(=O)CCCCN(CCc1ccccc1OCc2ccc(CCc3ccccc3)cc2)Cc4ccc(cc4)C(O)=O
SMILES OpenEye OEToolkits 1.7.0 c1ccc(cc1)CCc2ccc(cc2)COc3ccccc3CCN(CCCCC(=O)O)Cc4ccc(cc4)C(=O)O
Canonical SMILES CACTVS 3.352 OC(=O)CCCCN(CCc1ccccc1OCc2ccc(CCc3ccccc3)cc2)Cc4ccc(cc4)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.0 c1ccc(cc1)CCc2ccc(cc2)COc3ccccc3CC[N@@](CCCCC(=O)O)Cc4ccc(cc4)C(=O)O

IUPAC InChI

InChI=1S/C36H39NO5/c38-35(39)12-6-7-24-37(26-30-19-21-33(22-20-30)36(40)41)25-23-32-10-4-5-11-34(32)42-27-31-17-15-29(16-18-31)14-13-28-8-2-1-3-9-28/h1-5,8-11,15-22H,6-7,12-14,23-27H2,(H,38,39)(H,40,41)

IUPAC InChI key

WPYWMXNXEZFMAK-UHFFFAOYSA-N
Z90

wwPDB Information

Atom count

81 (42 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-01-23

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



Z90 : Atoms of Molecule

Total Number of Atoms: 81
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OAA O OAA N N N 0 -1.618 -6.383 2.616
2 OAB O OAB N N N 0 9.375 -1.894 -1.056
3 OAC O OAC N N N 0 -2.359 -4.337 2.233
4 OAD O OAD N N N 0 9.266 0.016 -2.181
5 CAE C CAE N Y N 0 -10.157 -1.327 -1.749
6 CAF C CAF N Y N 0 -9.915 -0.909 -0.454
7 CAG C CAG N Y N 0 -9.307 -0.942 -2.77
8 CAH C CAH N Y N 0 3.644 4.748 1.793
9 CAI C CAI N Y N 0 2.516 5.484 1.483
10 CAJ C CAJ N Y N 0 -8.826 -0.104 -0.179
11 CAK C CAK N Y N 0 -8.221 -0.132 -2.496
12 CAL C CAL N Y N 0 3.591 3.366 1.801
13 CAM C CAM N Y N 0 1.331 4.84 1.181
14 CAN C CAN N Y N 0 -4.151 1.583 1.024
15 CAO C CAO N Y N 0 -3.543 1.55 -1.291
16 CAP C CAP N Y N 0 -3.058 2.384 1.3
17 CAQ C CAQ N Y N 0 -2.447 2.347 -1.015
18 CAR C CAR N Y N 0 5.236 -2.246 -0.715
19 CAS C CAS N Y N 0 5.047 -0.188 -1.936
20 CAT C CAT N Y N 0 6.611 -2.178 -0.799
21 CAU C CAU N Y N 0 6.421 -0.102 -2.019
22 CAV C CAV N N N 0 -0.145 -3.19 1.334
23 CAW C CAW N N N 0 1.232 -2.733 0.847
24 CAX C CAX N N N 0 -0.08 -4.666 1.733
25 CAY C CAY N N N 0 -6.79 1.161 -0.9
26 CAZ C CAZ N N N 0 -5.579 0.286 -0.57
27 CBA C CBA N N N 0 2.351 1.212 1.514
28 CBB C CBB N N N 0 1.167 -1.257 0.448
29 CBC C CBC N N N 0 2.571 0.684 0.095
30 CBD C CBD N N N 0 -1.016 3.639 0.58
31 CBE C CBE N N N 0 2.953 -1.335 -1.185
32 OBF O OBF N N N 0 0.112 2.818 0.891
33 CBG C CBG N N N 0 -1.436 -5.116 2.212
34 CBH C CBH N N N 0 8.687 -1.023 -1.548
35 CBI C CBI N Y N 0 -7.977 0.282 -1.2
36 CBJ C CBJ N Y N 0 -4.391 1.164 -0.271
37 CBK C CBK N Y N 0 -2.206 2.766 0.28
38 CBL C CBL N Y N 0 4.455 -1.254 -1.281
39 CBM C CBM N Y N 0 7.215 -1.102 -1.454
40 CBN C CBN N Y N 0 2.408 2.718 1.505
41 CBO C CBO N Y N 0 1.275 3.454 1.188
42 NBP N NBP N N N 0 2.515 -0.784 0.104
43 HOAA H HOAA N N N 0 -2.505 -6.625 2.916
44 HOAD H HOAD N N N 0 10.233 0.025 -2.217
45 HAE H HAE N N N 0 -11.006 -1.959 -1.963
46 HAF H HAF N N N 0 -10.579 -1.21 0.343
47 HAG H HAG N N N 0 -9.493 -1.273 -3.781
48 HAH H HAH N N N 0 4.57 5.253 2.024
49 HAI H HAI N N N 0 2.56 6.563 1.477
50 HAJ H HAJ N N N 0 -8.638 0.223 0.832
51 HAK H HAK N N N 0 -7.558 0.17 -3.293
52 HAL H HAL N N N 0 4.475 2.794 2.04
53 HAM H HAM N N N 0 0.449 5.415 0.939
54 HAN H HAN N N N 0 -4.814 1.281 1.821
55 HAO H HAO N N N 0 -3.731 1.223 -2.303
56 HAP H HAP N N N 0 -2.87 2.712 2.312
57 HAQ H HAQ N N N 0 -1.779 2.641 -1.811
58 HAR H HAR N N N 0 4.768 -3.077 -0.209
59 HAS H HAS N N N 0 4.431 0.585 -2.372
60 HAT H HAT N N N 0 7.22 -2.955 -0.36
61 HAU H HAU N N N 0 6.882 0.737 -2.52
62 HAV H HAV N N N 0 -0.442 -2.593 2.197
63 HAVA H HAVA N N N 0 -0.874 -3.061 0.535
64 HAW H HAW N N N 0 1.961 -2.862 1.646
65 HAWA H HAWA N N N 0 1.529 -3.329 -0.015
66 HAX H HAX N N N 0 0.217 -5.262 0.87
67 HAXA H HAXA N N N 0 0.649 -4.794 2.532
68 HAY H HAY N N N 0 -7.018 1.802 -0.049
69 HAYA H HAYA N N N 0 -6.566 1.778 -1.771
70 HAZ H HAZ N N N 0 -5.803 -0.331 0.3
71 HAZA H HAZA N N N 0 -5.351 -0.355 -1.422
72 HBA H HBA N N N 0 1.375 0.888 1.875
73 HBAA H HBAA N N N 0 3.129 0.823 2.171
74 HBB H HBB N N N 0 0.511 -1.142 -0.414
75 HBBA H HBBA N N N 0 0.779 -0.672 1.282
76 HBC H HBC N N N 0 1.793 1.074 -0.562
77 HBCA H HBCA N N N 0 3.547 1.009 -0.266
78 HBD H HBD N N N 0 -1.242 4.283 1.431
79 HBDA H HBDA N N N 0 -0.788 4.255 -0.29
80 HBE H HBE N N N 0 2.506 -0.762 -1.997
81 HBEA H HBEA N N N 0 2.64 -2.376 -1.26



Z90 : Chemical Bonds

Total Number of Bonds: 84
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CBG OAA C O sing 1.34 N N
2 OAA HOAA O H sing 0.97 N N
3 CBH OAB C O doub 1.21 N N
4 OAC CBG O C doub 1.21 N N
5 CBH OAD C O sing 1.35 N N
6 OAD HOAD O H sing 0.97 N N
7 CAF CAE C C doub 1.38 N Y
8 CAE CAG C C sing 1.38 N Y
9 CAE HAE C H sing 1.08 N N
10 CAJ CAF C C sing 1.38 N Y
11 CAF HAF C H sing 1.08 N N
12 CAK CAG C C doub 1.38 N Y
13 CAG HAG C H sing 1.08 N N
14 CAI CAH C C doub 1.38 N Y
15 CAH CAL C C sing 1.38 N Y
16 CAH HAH C H sing 1.08 N N
17 CAI CAM C C sing 1.38 N Y
18 CAI HAI C H sing 1.08 N N
19 CAJ CBI C C doub 1.38 N Y
20 CAJ HAJ C H sing 1.08 N N
21 CBI CAK C C sing 1.38 N Y
22 CAK HAK C H sing 1.08 N N
23 CAL CBN C C doub 1.38 N Y
24 CAL HAL C H sing 1.08 N N
25 CAM CBO C C doub 1.39 N Y
26 CAM HAM C H sing 1.08 N N
27 CAP CAN C C doub 1.38 N Y
28 CAN CBJ C C sing 1.38 N Y
29 CAN HAN C H sing 1.08 N N
30 CAQ CAO C C sing 1.38 N Y
31 CBJ CAO C C doub 1.38 N Y
32 CAO HAO C H sing 1.08 N N
33 CAP CBK C C sing 1.38 N Y
34 CAP HAP C H sing 1.08 N N
35 CBK CAQ C C doub 1.38 N Y
36 CAQ HAQ C H sing 1.08 N N
37 CBL CAR C C doub 1.38 N Y
38 CAR CAT C C sing 1.38 N Y
39 CAR HAR C H sing 1.08 N N
40 CBL CAS C C sing 1.38 N Y
41 CAS CAU C C doub 1.38 N Y
42 CAS HAS C H sing 1.08 N N
43 CAT CBM C C doub 1.4 N Y
44 CAT HAT C H sing 1.08 N N
45 CAU CBM C C sing 1.4 N Y
46 CAU HAU C H sing 1.08 N N
47 CAW CAV C C sing 1.53 N N
48 CAX CAV C C sing 1.53 N N
49 CAV HAV C H sing 1.09 N N
50 CAV HAVA C H sing 1.09 N N
51 CAW CBB C C sing 1.53 N N
52 CAW HAW C H sing 1.09 N N
53 CAW HAWA C H sing 1.09 N N
54 CAX CBG C C sing 1.51 N N
55 CAX HAX C H sing 1.09 N N
56 CAX HAXA C H sing 1.09 N N
57 CAZ CAY C C sing 1.53 N N
58 CAY CBI C C sing 1.51 N N
59 CAY HAY C H sing 1.09 N N
60 CAY HAYA C H sing 1.09 N N
61 CBJ CAZ C C sing 1.51 N N
62 CAZ HAZ C H sing 1.09 N N
63 CAZ HAZA C H sing 1.09 N N
64 CBN CBA C C sing 1.51 N N
65 CBA CBC C C sing 1.53 N N
66 CBA HBA C H sing 1.09 N N
67 CBA HBAA C H sing 1.09 N N
68 NBP CBB N C sing 1.47 N N
69 CBB HBB C H sing 1.09 N N
70 CBB HBBA C H sing 1.09 N N
71 CBC NBP C N sing 1.47 N N
72 CBC HBC C H sing 1.09 N N
73 CBC HBCA C H sing 1.09 N N
74 OBF CBD O C sing 1.43 N N
75 CBD CBK C C sing 1.51 N N
76 CBD HBD C H sing 1.09 N N
77 CBD HBDA C H sing 1.09 N N
78 NBP CBE N C sing 1.47 N N
79 CBE CBL C C sing 1.51 N N
80 CBE HBE C H sing 1.09 N N
81 CBE HBEA C H sing 1.09 N N
82 CBO OBF C O sing 1.36 N N
83 CBM CBH C C sing 1.48 N N
84 CBO CBN C C sing 1.39 N Y



Z90 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
Z90 3l6j Open in New Window Bound ligand 2 1
Z90 5mnw Open in New Window Bound ligand 1 1