Chemical Components in the PDB

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5IK : Summary

Code

5IK

One-letter code

X

Molecule name

4-(hydroxymethyl)-7-[[4-[[methyl-(phenylmethyl)amino]methyl]phenyl]methoxy]chromen-2-one

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 4-(hydroxymethyl)-7-[[4-[[methyl-(phenylmethyl)amino]methyl]phenyl]methoxy]chromen-2-one

Formula

C26 H25 N O4

Formal charge

0

Molecular weight

415.481 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN(Cc1ccccc1)Cc2ccc(COc3ccc4C(=CC(=O)Oc4c3)CO)cc2
SMILES OpenEye OEToolkits 2.0.7 CN(Cc1ccccc1)Cc2ccc(cc2)COc3ccc4c(c3)OC(=O)C=C4CO
Canonical SMILES CACTVS 3.385 CN(Cc1ccccc1)Cc2ccc(COc3ccc4C(=CC(=O)Oc4c3)CO)cc2
Canonical SMILES OpenEye OEToolkits 2.0.7 CN(Cc1ccccc1)Cc2ccc(cc2)COc3ccc4c(c3)OC(=O)C=C4CO

IUPAC InChI

InChI=1S/C26H25NO4/c1-27(15-19-5-3-2-4-6-19)16-20-7-9-21(10-8-20)18-30-23-11-12-24-22(17-28)13-26(29)31-25(24)14-23/h2-14,28H,15-18H2,1H3

IUPAC InChI key

RTJRBYKZQSYWCM-UHFFFAOYSA-N
5IK

wwPDB Information

Atom count

56 (31 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-07-12

Last modified at

2022-04-01

Status

Released

Obsoleted

Not Assigned



5IK : Atoms of Molecule

Total Number of Atoms: 56
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CAG C C1 N Y N 0 -8.509 -0.337 -0.926
2 CAE C C2 N Y N 0 -9.395 -1.395 -0.836
3 CAD C C3 N Y N 0 -9.633 -1.995 0.387
4 CAF C C4 N Y N 0 -8.986 -1.536 1.519
5 CAH C C5 N Y N 0 -8.101 -0.479 1.429
6 CAX C C6 N Y N 0 -7.858 0.117 0.206
7 CAS C C7 N N N 0 -6.892 1.27 0.108
8 NBE N N1 N N N 0 -5.54 0.756 -0.15
9 CAA C C8 N N N 0 -5.462 0.121 -1.473
10 CAT C C9 N N N 0 -4.538 1.822 -0.018
11 CAY C C10 N Y N 0 -3.157 1.219 -0.044
12 CAL C C11 N Y N 0 -2.494 1.063 -1.247
13 CAJ C C12 N Y N 0 -1.228 0.509 -1.272
14 CAK C C13 N Y N 0 -2.551 0.827 1.135
15 CAI C C14 N Y N 0 -1.284 0.274 1.11
16 CAW C C15 N Y N 0 -0.624 0.112 -0.094
17 CAR C C16 N N N 0 0.756 -0.492 -0.12
18 OAU O O1 N N N 0 1.732 0.544 0.009
19 CAZ C C17 N Y N 0 3.036 0.167 0.003
20 CAP C C18 N Y N 0 4.029 1.124 0.13
21 CAM C C19 N Y N 0 3.365 -1.182 -0.126
22 CAN C C20 N Y N 0 4.671 -1.577 -0.133
23 CBD C C21 N Y N 0 5.687 -0.622 -0.011
24 CBC C C22 N Y N 0 5.361 0.739 0.13
25 OAV O O2 N N N 0 6.344 1.657 0.247
26 CBB C C23 N N N 0 7.639 1.303 0.233
27 OAB O O3 N N N 0 8.491 2.167 0.332
28 CAO C C24 N N N 0 8.037 -0.043 0.096
29 CBA C C25 N N N 0 7.097 -1.018 -0.015
30 CAQ C C26 N N N 0 7.495 -2.463 -0.163
31 OAC O O4 N N N 0 8.92 -2.568 -0.161
32 H1 H H1 N N N 0 -8.323 0.131 -1.881
33 H2 H H2 N N N 0 -9.9 -1.753 -1.72
34 H3 H H3 N N N 0 -10.325 -2.821 0.457
35 H4 H H4 N N N 0 -9.173 -2.005 2.474
36 H5 H H5 N N N 0 -7.592 -0.124 2.313
37 H6 H H6 N N N 0 -7.193 1.927 -0.708
38 H7 H H7 N N N 0 -6.896 1.828 1.044
39 H9 H H9 N N N 0 -5.711 0.852 -2.242
40 H10 H H10 N N N 0 -4.451 -0.25 -1.638
41 H11 H H11 N N N 0 -6.166 -0.709 -1.519
42 H12 H H12 N N N 0 -4.644 2.525 -0.844
43 H13 H H13 N N N 0 -4.688 2.346 0.927
44 H14 H H14 N N N 0 -2.966 1.373 -2.168
45 H15 H H15 N N N 0 -0.71 0.387 -2.212
46 H16 H H16 N N N 0 -3.067 0.953 2.075
47 H17 H H17 N N N 0 -0.811 -0.031 2.031
48 H18 H H18 N N N 0 0.861 -1.195 0.706
49 H19 H H19 N N N 0 0.905 -1.016 -1.065
50 H20 H H20 N N N 0 3.766 2.167 0.228
51 H21 H H21 N N N 0 2.58 -1.919 -0.22
52 H22 H H22 N N N 0 4.919 -2.623 -0.232
53 H23 H H23 N N N 0 9.086 -0.299 0.088
54 H24 H H24 N N N 0 7.087 -3.039 0.668
55 H25 H H25 N N N 0 7.104 -2.854 -1.102
56 H26 H H26 N N N 0 9.249 -3.473 -0.252



5IK : Chemical Bonds

Total Number of Bonds: 59
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAB CBB O C doub 1.22 N N
2 CBB CAO C C sing 1.41 N N
3 CBB OAV C O sing 1.34 N N
4 CAO CBA C C doub 1.36 N N
5 OAC CAQ O C sing 1.43 N N
6 OAV CBC O C sing 1.35 N N
7 CBA CAQ C C sing 1.51 N N
8 CBA CBD C C sing 1.46 N N
9 CBC CBD C C doub 1.41 N Y
10 CBC CAP C C sing 1.39 N Y
11 CBD CAN C C sing 1.4 N Y
12 CAP CAZ C C doub 1.38 N Y
13 CAN CAM C C doub 1.36 N Y
14 CAZ CAM C C sing 1.39 N Y
15 CAZ OAU C O sing 1.36 N N
16 CAR OAU C O sing 1.43 N N
17 CAR CAW C C sing 1.51 N N
18 CAW CAJ C C doub 1.38 N Y
19 CAW CAI C C sing 1.38 N Y
20 CAJ CAL C C sing 1.38 N Y
21 CAI CAK C C doub 1.38 N Y
22 CAL CAY C C doub 1.38 N Y
23 CAK CAY C C sing 1.38 N Y
24 CAA NBE C N sing 1.47 N N
25 CAY CAT C C sing 1.51 N N
26 CAT NBE C N sing 1.47 N N
27 NBE CAS N C sing 1.47 N N
28 CAS CAX C C sing 1.51 N N
29 CAH CAX C C doub 1.38 N Y
30 CAH CAF C C sing 1.38 N Y
31 CAX CAG C C sing 1.38 N Y
32 CAF CAD C C doub 1.38 N Y
33 CAG CAE C C doub 1.38 N Y
34 CAD CAE C C sing 1.38 N Y
35 CAG H1 C H sing 1.08 N N
36 CAE H2 C H sing 1.08 N N
37 CAD H3 C H sing 1.08 N N
38 CAF H4 C H sing 1.08 N N
39 CAH H5 C H sing 1.08 N N
40 CAS H6 C H sing 1.09 N N
41 CAS H7 C H sing 1.09 N N
42 CAA H9 C H sing 1.09 N N
43 CAA H10 C H sing 1.09 N N
44 CAA H11 C H sing 1.09 N N
45 CAT H12 C H sing 1.09 N N
46 CAT H13 C H sing 1.09 N N
47 CAL H14 C H sing 1.08 N N
48 CAJ H15 C H sing 1.08 N N
49 CAK H16 C H sing 1.08 N N
50 CAI H17 C H sing 1.08 N N
51 CAR H18 C H sing 1.09 N N
52 CAR H19 C H sing 1.09 N N
53 CAP H20 C H sing 1.08 N N
54 CAM H21 C H sing 1.08 N N
55 CAN H22 C H sing 1.08 N N
56 CAO H23 C H sing 1.08 N N
57 CAQ H24 C H sing 1.09 N N
58 CAQ H25 C H sing 1.09 N N
59 OAC H26 O H sing 0.97 N N



5IK : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
5IK 7p4f Open in New Window Bound ligand 2 1
5IK 7qak Open in New Window Bound ligand 2 1