Chemical Components in the PDB

pdbe.org/chem
spacer

1RK : Summary

Code

1RK

One-letter code

X

Molecule name

6-methoxy-5-({(3S)-3-[(N-methyl-L-alanyl)amino]-4-oxo-2',3,3',4,5',6'-hexahydro-5H-spiro[1,5-benzoxazepine-2,4'-pyran]-5-yl}methyl)naphthalene-2-carboxylic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 6-methoxy-5-({(3S)-3-[(N-methyl-L-alanyl)amino]-4-oxo-2',3,3',4,5',6'-hexahydro-5H-spiro[1,5-benzoxazepine-2,4'-pyran]-5-yl}methyl)naphthalene-2-carboxylic acid
OpenEye OEToolkits 1.7.6 6-methoxy-5-[[(3S)-3-[[(2S)-2-(methylamino)propanoyl]amino]-4-oxidanylidene-spiro[3H-1,5-benzoxazepine-2,4'-oxane]-5-yl]methyl]naphthalene-2-carboxylic acid

Formula

C30 H33 N3 O7

Formal charge

0

Molecular weight

547.599 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)c1ccc2c(c1)ccc(OC)c2CN3c5c(OC4(C(C3=O)NC(=O)C(NC)C)CCOCC4)cccc5
SMILES CACTVS 3.370 CN[CH](C)C(=O)N[CH]1C(=O)N(Cc2c(OC)ccc3cc(ccc23)C(O)=O)c4ccccc4OC15CCOCC5
SMILES OpenEye OEToolkits 1.7.6 CC(C(=O)NC1C(=O)N(c2ccccc2OC13CCOCC3)Cc4c5ccc(cc5ccc4OC)C(=O)O)NC
Canonical SMILES CACTVS 3.370 CN[C@@H](C)C(=O)N[C@@H]1C(=O)N(Cc2c(OC)ccc3cc(ccc23)C(O)=O)c4ccccc4OC15CCOCC5
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@@H](C(=O)N[C@@H]1C(=O)N(c2ccccc2OC13CCOCC3)Cc4c5ccc(cc5ccc4OC)C(=O)O)NC

IUPAC InChI

InChI=1S/C30H33N3O7/c1-18(31-2)27(34)32-26-28(35)33(23-6-4-5-7-25(23)40-30(26)12-14-39-15-13-30)17-22-21-10-8-20(29(36)37)16-19(21)9-11-24(22)38-3/h4-11,16,18,26,31H,12-15,17H2,1-3H3,(H,32,34)(H,36,37)/t18-,26+/m0/s1

IUPAC InChI key

PXBQMHIHZVFKSD-HFJWLAOPSA-N
1RK

wwPDB Information

Atom count

73 (40 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-05-08

Last modified at

2013-11-22

Status

Released

Obsoleted

Not Assigned



1RK : Atoms of Molecule

Total Number of Atoms: 73
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C29 C C29 N N N 0 1.316 -4.789 1.89
2 O28 O O28 N N N 0 1.028 -3.392 1.968
3 C27 C C27 N Y N 0 1.978 -2.539 1.505
4 C30 C C30 N Y N 0 3.169 -3.05 0.978
5 C31 C C31 N Y N 0 4.137 -2.221 0.508
6 C32 C C32 N Y N 0 3.946 -0.827 0.548
7 C34 C C34 N Y N 0 4.929 0.05 0.069
8 C35 C C35 N Y N 0 4.709 1.418 0.124
9 C38 C C38 N N N 0 5.74 2.346 -0.379
10 O40 O O40 N N N 0 6.777 1.912 -0.838
11 O39 O O39 N N N 0 5.53 3.677 -0.329
12 C36 C C36 N Y N 0 3.509 1.927 0.654
13 C37 C C37 N Y N 0 2.547 1.093 1.123
14 C33 C C33 N Y N 0 2.741 -0.301 1.081
15 C15 C C15 N Y N 0 1.756 -1.181 1.555
16 C14 C C14 N N N 0 0.467 -0.644 2.119
17 N13 N N13 N N N 0 -0.473 -0.381 1.026
18 C16 C C16 N N N 0 -1.276 -1.366 0.565
19 O17 O O17 N N N 0 -1.179 -2.49 1.011
20 C12 C C12 N Y N 0 -0.552 0.895 0.451
21 C21 C C21 N Y N 0 -0.652 2.023 1.248
22 C19 C C19 N Y N 0 -0.722 3.274 0.663
23 C20 C C20 N Y N 0 -0.692 3.401 -0.713
24 C18 C C18 N Y N 0 -0.594 2.277 -1.514
25 C11 C C11 N Y N 0 -0.524 1.021 -0.937
26 O10 O O10 N N N 0 -0.434 -0.09 -1.713
27 C9 C C9 N N N 0 -1.608 -0.886 -1.853
28 C22 C C22 N N N 0 -1.226 -2.263 -2.408
29 C23 C C23 N N N 0 -0.614 -2.091 -3.8
30 O24 O O24 N N N 0 -1.55 -1.426 -4.651
31 C25 C C25 N N N 0 -1.911 -0.116 -4.208
32 C26 C C26 N N N 0 -2.572 -0.207 -2.831
33 C7 C C7 S N N 0 -2.293 -1.062 -0.505
34 N6 N N6 N N N 0 -3.002 0.171 -0.155
35 C5 C C5 N N N 0 -4.056 0.128 0.683
36 O8 O O8 N N N 0 -4.418 -0.932 1.147
37 C3 C C3 S N N 0 -4.786 1.397 1.042
38 C4 C C4 N N N 0 -3.816 2.369 1.718
39 N1 N N1 N N N 0 -5.887 1.085 1.962
40 C2 C C2 N N N 0 -6.946 2.099 1.88
41 H1 H H1 N N N 0 1.479 -5.069 0.849
42 H2 H H2 N N N 0 2.214 -5.008 2.469
43 H3 H H3 N N N 0 0.477 -5.357 2.292
44 H4 H H4 N N N 0 3.321 -4.119 0.944
45 H5 H H5 N N N 0 5.051 -2.63 0.104
46 H6 H H6 N N N 0 5.852 -0.337 -0.339
47 H7 H H7 N N N 0 6.234 4.245 -0.669
48 H8 H H8 N N N 0 3.352 2.995 0.689
49 H9 H H9 N N N 0 1.631 1.498 1.527
50 H10 H H10 N N N 0 0.035 -1.376 2.801
51 H11 H H11 N N N 0 0.664 0.283 2.658
52 H12 H H12 N N N 0 -0.676 1.926 2.323
53 H13 H H13 N N N 0 -0.799 4.155 1.284
54 H14 H H14 N N N 0 -0.746 4.38 -1.164
55 H15 H H15 N N N 0 -0.572 2.381 -2.589
56 H16 H H16 N N N 0 -0.498 -2.733 -1.746
57 H17 H H17 N N N 0 -2.116 -2.888 -2.475
58 H18 H H18 N N N 0 0.296 -1.496 -3.727
59 H19 H H19 N N N 0 -0.376 -3.07 -4.216
60 H20 H H20 N N N 0 -1.016 0.504 -4.141
61 H21 H H21 N N N 0 -2.608 0.328 -4.918
62 H22 H H22 N N N 0 -3.488 -0.794 -2.906
63 H23 H H23 N N N 0 -2.809 0.795 -2.474
64 H24 H H24 N N N 0 -3.007 -1.882 -0.567
65 H25 H H25 N N N 0 -2.712 1.019 -0.527
66 H26 H H26 N N N 0 -5.187 1.854 0.137
67 H27 H H27 N N N 0 -4.344 3.286 1.978
68 H28 H H28 N N N 0 -3.415 1.911 2.622
69 H29 H H29 N N N 0 -2.999 2.6 1.035
70 H30 H H30 N N N 0 -5.551 0.989 2.909
71 H32 H H32 N N N 0 -6.536 3.075 2.144
72 H33 H H33 N N N 0 -7.339 2.133 0.864
73 H34 H H34 N N N 0 -7.749 1.844 2.571



1RK : Chemical Bonds

Total Number of Bonds: 77
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C2 N1 C N sing 1.4684689 N N
2 N1 C3 N C sing 1.4683137 N N
3 O8 C5 O C doub 1.2124108 N N
4 C3 C5 C C sing 1.5073626 N N
5 C3 C4 C C sing 1.530575 N N
6 C5 N6 C N sing 1.3472227 N N
7 C19 C20 C C doub 1.382174 N Y
8 C19 C21 C C sing 1.3827964 N Y
9 C20 C18 C C sing 1.3836838 N Y
10 C21 C12 C C doub 1.3847718 N Y
11 C22 C23 C C sing 1.5302914 N N
12 C22 C9 C C sing 1.5329964 N N
13 C18 C11 C C doub 1.3839672 N Y
14 N6 C7 N C sing 1.4647423 N N
15 C23 O24 C O sing 1.4291683 N N
16 C7 C9 C C sing 1.5222697 N N
17 C7 C16 C C sing 1.5071845 N N
18 C12 C11 C C sing 1.3939885 N Y
19 C12 N13 C N sing 1.4017996 N N
20 C11 O10 C O sing 1.3581594 N N
21 C9 O10 C O sing 1.4253042 N N
22 C9 C26 C C sing 1.5319338 N N
23 C29 O28 C O sing 1.4285086 N N
24 N13 C16 N C sing 1.3518709 N N
25 N13 C14 N C sing 1.4654071 N N
26 C16 O17 C O doub 1.2131368 N N
27 O28 C27 O C sing 1.3581156 N N
28 O24 C25 O C sing 1.4292201 N N
29 C14 C15 C C sing 1.5059834 N N
30 C26 C25 C C sing 1.5301409 N N
31 C27 C15 C C doub 1.3769343 N Y
32 C27 C30 C C sing 1.3990464 N Y
33 C15 C33 C C sing 1.4033178 N Y
34 C30 C31 C C doub 1.3583685 N Y
35 C33 C37 C C doub 1.408061 N Y
36 C33 C32 C C sing 1.4187284 N Y
37 C37 C36 C C sing 1.3568202 N Y
38 C31 C32 C C sing 1.4075927 N Y
39 C32 C34 C C doub 1.4017342 N Y
40 C36 C35 C C doub 1.407118 N Y
41 C34 C35 C C sing 1.3866683 N Y
42 C35 C38 C C sing 1.4755182 N N
43 C38 O40 C O doub 1.2142512 N N
44 C38 O39 C O sing 1.348392 N N
45 C29 H1 C H sing 1.0902523 N N
46 C29 H2 C H sing 1.0906906 N N
47 C29 H3 C H sing 1.0900224 N N
48 C30 H4 C H sing 1.0802875 N N
49 C31 H5 C H sing 1.0797652 N N
50 C34 H6 C H sing 1.0808154 N N
51 O39 H7 O H sing 0.96635395 N N
52 C36 H8 C H sing 1.0800453 N N
53 C37 H9 C H sing 1.0799524 N N
54 C14 H10 C H sing 1.0897578 N N
55 C14 H11 C H sing 1.0902563 N N
56 C21 H12 C H sing 1.0796342 N N
57 C19 H13 C H sing 1.080616 N N
58 C20 H14 C H sing 1.0792395 N N
59 C18 H15 C H sing 1.080243 N N
60 C22 H16 C H sing 1.0904715 N N
61 C22 H17 C H sing 1.0895935 N N
62 C23 H18 C H sing 1.0897037 N N
63 C23 H19 C H sing 1.0900187 N N
64 C25 H20 C H sing 1.0908318 N N
65 C25 H21 C H sing 1.0895159 N N
66 C26 H22 C H sing 1.0905274 N N
67 C26 H23 C H sing 1.0897807 N N
68 C7 H24 C H sing 1.0890546 N N
69 N6 H25 N H sing 0.97035456 N N
70 C3 H26 C H sing 1.0902637 N N
71 C4 H27 C H sing 1.0896206 N N
72 C4 H28 C H sing 1.0898536 N N
73 C4 H29 C H sing 1.0896509 N N
74 N1 H30 N H sing 1.0094162 N N
75 C2 H32 C H sing 1.0910417 N N
76 C2 H33 C H sing 1.0898904 N N
77 C2 H34 C H sing 1.0896399 N N



1RK : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
1RK 4kjv Open in New Window Bound ligand 1 1