Chemical Components in the PDB

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9YB : Summary

Code

9YB

One-letter code

X

Molecule name

(3~{R})-3-[[1-(2-hydroxyethyl)-5-[(4-methoxynaphthalen-1-yl)methyl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-3-yl]carbonylamino]-3-phenyl-propanoic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 (3~{R})-3-[[1-(2-hydroxyethyl)-5-[(4-methoxynaphthalen-1-yl)methyl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-3-yl]carbonylamino]-3-phenyl-propanoic acid

Formula

C30 H32 N4 O5

Formal charge

0

Molecular weight

528.599 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 COc1ccc(CN2CCc3n(CCO)nc(C(=O)N[CH](CC(O)=O)c4ccccc4)c3C2)c5ccccc15
SMILES OpenEye OEToolkits 2.0.6 COc1ccc(c2c1cccc2)CN3CCc4c(c(nn4CCO)C(=O)NC(CC(=O)O)c5ccccc5)C3
Canonical SMILES CACTVS 3.385 COc1ccc(CN2CCc3n(CCO)nc(C(=O)N[C@H](CC(O)=O)c4ccccc4)c3C2)c5ccccc15
Canonical SMILES OpenEye OEToolkits 2.0.6 COc1ccc(c2c1cccc2)CN3CCc4c(c(nn4CCO)C(=O)N[C@H](CC(=O)O)c5ccccc5)C3

IUPAC InChI

InChI=1S/C30H32N4O5/c1-39-27-12-11-21(22-9-5-6-10-23(22)27)18-33-14-13-26-24(19-33)29(32-34(26)15-16-35)30(38)31-25(17-28(36)37)20-7-3-2-4-8-20/h2-12,25,35H,13-19H2,1H3,(H,31,38)(H,36,37)/t25-/m1/s1

IUPAC InChI key

FEINFPMXJVPOSJ-RUZDIDTESA-N
9YB

wwPDB Information

Atom count

71 (39 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-08-01

Last modified at

2019-03-01

Status

Released

Obsoleted

Not Assigned



9YB : Atoms of Molecule

Total Number of Atoms: 71
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N Y N 0 -6.41 -0.415 -1.36
2 C5 C C2 N Y N 0 -5.089 -0.375 -1.8
3 C6 C C3 N Y N 0 -5.944 1.329 0.22
4 C11 C C4 N Y N 0 -4.6 1.362 -0.227
5 C7 C C5 N Y N 0 -6.352 2.202 1.241
6 C8 C C6 N Y N 0 -5.454 3.067 1.787
7 C9 C C7 N Y N 0 -4.132 3.1 1.348
8 C10 C C8 N Y N 0 -3.701 2.268 0.36
9 C12 C C9 N Y N 0 -4.192 0.491 -1.252
10 C13 C C10 N N N 0 -2.768 0.515 -1.744
11 C3 C C11 N Y N 0 -6.845 0.419 -0.369
12 C1 C C12 N N N 0 -8.991 -0.576 -0.6
13 O2 O O1 N N N 0 -8.138 0.371 0.045
14 N14 N N1 N N N 0 -1.917 -0.241 -0.815
15 C15 C C13 N N N 0 -0.489 -0.043 -1.127
16 C16 C C14 N Y N 0 0.316 -0.933 -0.221
17 C17 C C15 N N N 0 -2.275 -1.666 -0.813
18 C18 C C16 N N N 0 -1.663 -2.355 0.415
19 C19 C C17 N Y N 0 -0.206 -1.973 0.479
20 N20 N N2 N Y N 0 0.797 -2.527 1.175
21 C21 C C18 N N N 0 0.662 -3.681 2.068
22 C22 C C19 N N N 0 0.892 -4.969 1.275
23 O23 O O2 N N N 0 0.761 -6.094 2.146
24 N24 N N3 N Y N 0 1.896 -1.895 0.943
25 C25 C C20 N Y N 0 1.683 -0.904 0.095
26 C26 C C21 N N N 0 2.687 0.05 -0.419
27 O27 O O3 N N N 0 2.354 0.922 -1.199
28 C30 C C23 N N N 0 6.355 0.146 -0.536
29 N28 N N4 N N N 0 3.972 -0.046 -0.024
30 C29 C C22 R N N 0 4.988 0.827 -0.616
31 C37 C C24 N N N 0 6.354 -1.087 -1.403
32 O39 O O4 N N N 0 5.338 -1.435 -1.957
33 O38 O O5 N N N 0 7.482 -1.798 -1.559
34 C31 C C25 N Y N 0 5.031 2.131 0.139
35 C32 C C26 N Y N 0 4.92 2.136 1.516
36 C33 C C27 N Y N 0 4.96 3.332 2.209
37 C34 C C28 N Y N 0 5.11 4.523 1.523
38 C35 C C29 N Y N 0 5.222 4.518 0.145
39 C36 C C30 N Y N 0 5.187 3.321 -0.547
40 H1 H H1 N N N 0 -7.1 -1.112 -1.812
41 H2 H H2 N N N 0 -4.771 -1.042 -2.587
42 H3 H H3 N N N 0 -7.374 2.188 1.591
43 H4 H H4 N N N 0 -5.77 3.737 2.572
44 H5 H H5 N N N 0 -3.439 3.796 1.797
45 H6 H H6 N N N 0 -2.673 2.305 0.03
46 H7 H H7 N N N 0 -2.717 0.062 -2.734
47 H8 H H8 N N N 0 -2.42 1.547 -1.798
48 H9 H H9 N N N 0 -9.033 -0.36 -1.667
49 H10 H H10 N N N 0 -8.598 -1.582 -0.448
50 H11 H H11 N N N 0 -9.993 -0.51 -0.176
51 H13 H H13 N N N 0 -0.3 -0.31 -2.167
52 H14 H H14 N N N 0 -0.217 0.998 -0.958
53 H15 H H15 N N N 0 -3.36 -1.766 -0.782
54 H16 H H16 N N N 0 -1.894 -2.136 -1.72
55 H17 H H17 N N N 0 -2.172 -2.019 1.318
56 H18 H H18 N N N 0 -1.758 -3.436 0.317
57 H19 H H19 N N N 0 1.4 -3.61 2.867
58 H20 H H20 N N N 0 -0.339 -3.693 2.498
59 H21 H H21 N N N 0 0.154 -5.04 0.476
60 H22 H H22 N N N 0 1.893 -4.957 0.845
61 H23 H H23 N N N 0 0.894 -6.947 1.71
62 H24 H H24 N N N 0 4.224 -0.694 0.653
63 H25 H H25 N N N 0 4.738 1.02 -1.66
64 H26 H H26 N N N 0 7.125 0.835 -0.885
65 H27 H H27 N N N 0 6.561 -0.136 0.496
66 H28 H H28 N N N 0 7.431 -2.581 -2.125
67 H29 H H29 N N N 0 4.802 1.206 2.052
68 H30 H H30 N N N 0 4.872 3.336 3.285
69 H31 H H31 N N N 0 5.141 5.457 2.064
70 H32 H H32 N N N 0 5.339 5.448 -0.391
71 H33 H H33 N N N 0 5.278 3.317 -1.623



9YB : Chemical Bonds

Total Number of Bonds: 75
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C9 C8 C C doub 1.39 N Y
2 C9 C10 C C sing 1.36 N Y
3 C8 C7 C C sing 1.36 N Y
4 C10 C11 C C doub 1.4 N Y
5 O23 C22 O C sing 1.43 N N
6 C7 C6 C C doub 1.4 N Y
7 C17 C18 C C sing 1.54 N N
8 C17 N14 C N sing 1.47 N N
9 C18 C19 C C sing 1.51 N N
10 C11 C6 C C sing 1.42 N Y
11 C11 C12 C C sing 1.41 N Y
12 C22 C21 C C sing 1.53 N N
13 C13 N14 C N sing 1.47 N N
14 C13 C12 C C sing 1.51 N N
15 C6 C3 C C sing 1.41 N Y
16 N14 C15 N C sing 1.48 N N
17 C21 N20 C N sing 1.47 N N
18 C12 C5 C C doub 1.36 N Y
19 C19 N20 C N sing 1.34 N Y
20 C19 C16 C C doub 1.36 N Y
21 N20 N24 N N sing 1.29 N Y
22 C15 C16 C C sing 1.5 N N
23 C3 O2 C O sing 1.36 N N
24 C3 C4 C C doub 1.37 N Y
25 C16 C25 C C sing 1.4 N Y
26 C5 C4 C C sing 1.39 N Y
27 O2 C1 O C sing 1.43 N N
28 N24 C25 N C doub 1.32 N Y
29 C25 C26 C C sing 1.48 N N
30 C26 O27 C O doub 1.22 N N
31 C26 N28 C N sing 1.35 N N
32 O39 C37 O C doub 1.21 N N
33 N28 C29 N C sing 1.46 N N
34 C37 C30 C C sing 1.51 N N
35 C37 O38 C O sing 1.34 N N
36 C29 C30 C C sing 1.53 N N
37 C29 C31 C C sing 1.51 N N
38 C32 C31 C C doub 1.38 N Y
39 C32 C33 C C sing 1.38 N Y
40 C31 C36 C C sing 1.38 N Y
41 C33 C34 C C doub 1.38 N Y
42 C36 C35 C C doub 1.38 N Y
43 C34 C35 C C sing 1.38 N Y
44 C4 H1 C H sing 1.08 N N
45 C5 H2 C H sing 1.08 N N
46 C7 H3 C H sing 1.08 N N
47 C8 H4 C H sing 1.08 N N
48 C9 H5 C H sing 1.08 N N
49 C10 H6 C H sing 1.08 N N
50 C13 H7 C H sing 1.09 N N
51 C13 H8 C H sing 1.09 N N
52 C1 H9 C H sing 1.09 N N
53 C1 H10 C H sing 1.09 N N
54 C1 H11 C H sing 1.09 N N
55 C15 H13 C H sing 1.09 N N
56 C15 H14 C H sing 1.09 N N
57 C17 H15 C H sing 1.09 N N
58 C17 H16 C H sing 1.09 N N
59 C18 H17 C H sing 1.09 N N
60 C18 H18 C H sing 1.09 N N
61 C21 H19 C H sing 1.09 N N
62 C21 H20 C H sing 1.09 N N
63 C22 H21 C H sing 1.09 N N
64 C22 H22 C H sing 1.09 N N
65 O23 H23 O H sing 0.97 N N
66 N28 H24 N H sing 0.97 N N
67 C29 H25 C H sing 1.09 N N
68 C30 H26 C H sing 1.09 N N
69 C30 H27 C H sing 1.09 N N
70 O38 H28 O H sing 0.97 N N
71 C32 H29 C H sing 1.08 N N
72 C33 H30 C H sing 1.08 N N
73 C34 H31 C H sing 1.08 N N
74 C35 H32 C H sing 1.08 N N
75 C36 H33 C H sing 1.08 N N



9YB : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
9YB 5oml Open in New Window Bound ligand 4 1