Chemical Components in the PDB

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5PS : Summary

Code

5PS

One-letter code

X

Molecule name

(R)-N-(3-(1H-indol-3-yl)-1-oxo-1-(pyridin-4-ylamino)propan-2-yl)-3,3'-difluoro-(1,1'-biphenyl)-4-carboxamide

Systematic names

ProgramVersionName
ACDLabs 12.01 3,3'-difluoro-N-[(2R)-3-(1H-indol-3-yl)-1-oxo-1-(pyridin-4-ylamino)propan-2-yl]biphenyl-4-carboxamide
OpenEye OEToolkits 1.9.2 2-fluoranyl-4-(3-fluorophenyl)-N-[(2R)-3-(1H-indol-3-yl)-1-oxidanylidene-1-(pyridin-4-ylamino)propan-2-yl]benzamide

Formula

C29 H22 F2 N4 O2

Formal charge

0

Molecular weight

496.507 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Fc1cccc(c1)c2ccc(c(F)c2)C(=O)NC(C(=O)Nc3ccncc3)Cc5c4ccccc4nc5
SMILES CACTVS 3.385 Fc1cccc(c1)c2ccc(C(=O)N[CH](Cc3c[nH]c4ccccc34)C(=O)Nc5ccncc5)c(F)c2
SMILES OpenEye OEToolkits 1.9.2 c1ccc2c(c1)c(c[nH]2)CC(C(=O)Nc3ccncc3)NC(=O)c4ccc(cc4F)c5cccc(c5)F
Canonical SMILES CACTVS 3.385 Fc1cccc(c1)c2ccc(C(=O)N[C@H](Cc3c[nH]c4ccccc34)C(=O)Nc5ccncc5)c(F)c2
Canonical SMILES OpenEye OEToolkits 1.9.2 c1ccc2c(c1)c(c[nH]2)C[C@H](C(=O)Nc3ccncc3)NC(=O)c4ccc(cc4F)c5cccc(c5)F

IUPAC InChI

InChI=1S/C29H22F2N4O2/c30-21-5-3-4-18(14-21)19-8-9-24(25(31)15-19)28(36)35-27(29(37)34-22-10-12-32-13-11-22)16-20-17-33-26-7-2-1-6-23(20)26/h1-15,17,27,33H,16H2,(H,35,36)(H,32,34,37)/t27-/m1/s1

IUPAC InChI key

QLYGOABRPGBQNG-HHHXNRCGSA-N
5PS

wwPDB Information

Atom count

59 (37 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-07-16

Last modified at

2014-09-05

Status

Released

Obsoleted

Not Assigned



5PS : Atoms of Molecule

Total Number of Atoms: 59
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 -5.876 -3.075 -0.52
2 F1 F F1 N N N 0 8.198 -0.386 2.417
3 N1 N N1 N Y N 0 -5.852 -5.191 0.496
4 O1 O O1 N N N 0 -0.516 -0.356 -1.895
5 C2 C C2 N Y N 0 -6.406 -4.336 -0.342
6 F2 F F2 N N N 0 1.701 -0.715 -2.981
7 N2 N N2 N N N 0 -4.173 -1.443 0.051
8 O2 O O2 N N N 0 -2.124 -2.251 0.316
9 C3 C C3 N Y N 0 -4.776 -4.883 1.196
10 N3 N N3 N N N 0 -0.787 0.005 0.28
11 C4 C C4 N Y N 0 -4.185 -3.642 1.076
12 N4 N N4 N Y N 0 -1.099 4.193 1.427
13 C5 C C5 N Y N 0 -4.74 -2.71 0.201
14 C6 C C6 N N N 0 -2.841 -1.283 0.172
15 C8 C C8 N N N 0 -0.01 -0.226 -0.797
16 C9 C C9 N Y N 0 1.454 -0.32 -0.644
17 C10 C C10 N Y N 0 2.037 -0.17 0.617
18 C11 C C11 N Y N 0 3.403 -0.258 0.759
19 C12 C C12 N Y N 0 4.208 -0.497 -0.355
20 C13 C C13 N Y N 0 5.68 -0.591 -0.199
21 C14 C C14 N Y N 0 6.488 -0.829 -1.31
22 C15 C C15 N Y N 0 7.857 -0.916 -1.16
23 C16 C C16 N Y N 0 8.429 -0.767 0.09
24 C17 C C17 N Y N 0 7.633 -0.53 1.198
25 C18 C C18 N Y N 0 6.261 -0.435 1.058
26 C19 C C19 N Y N 0 3.631 -0.648 -1.615
27 C20 C C20 N Y N 0 2.261 -0.565 -1.761
28 C21 C C21 N N N 0 -2.82 0.942 1.266
29 C22 C C22 N Y N 0 -2.315 2.357 1.149
30 C23 C C23 N Y N 0 -1.251 2.88 1.779
31 C24 C C24 N Y N 0 -2.086 4.557 0.539
32 C25 C C25 N Y N 0 -2.392 5.743 -0.119
33 C26 C C26 N Y N 0 -3.475 5.795 -0.969
34 C27 C C27 N Y N 0 -4.267 4.673 -1.176
35 C28 C C28 N Y N 0 -3.984 3.497 -0.539
36 C29 C C29 N Y N 0 -2.891 3.423 0.326
37 C7 C C7 R N N 0 -2.241 0.099 0.128
38 H1 H H1 N N N 0 -6.332 -2.381 -1.211
39 H2 H H2 N N N 0 -7.286 -4.627 -0.897
40 H3 H H3 N N N 0 -4.353 -5.611 1.872
41 HA H HA N N N 0 -4.739 -0.679 -0.141
42 H4 H H4 N N N 0 -3.306 -3.396 1.652
43 HB H HB N N N 0 -0.383 0.109 1.156
44 H7 H H7 N N N 0 -2.477 0.567 -0.828
45 HC H HC N N N 0 -0.401 4.781 1.757
46 H23 H H23 N N N 0 -0.61 2.343 2.463
47 H10 H H10 N N N 0 1.416 0.015 1.481
48 H11 H H11 N N N 0 3.853 -0.142 1.734
49 H19 H H19 N N N 0 4.256 -0.833 -2.477
50 H14 H H14 N N N 0 6.042 -0.947 -2.287
51 H18 H H18 N N N 0 5.64 -0.245 1.921
52 H15 H H15 N N N 0 8.482 -1.101 -2.021
53 H16 H H16 N N N 0 9.501 -0.836 0.203
54 H211 H H211 N N N 0 -2.509 0.523 2.223
55 H212 H H212 N N N 0 -3.908 0.938 1.204
56 H25 H H25 N N N 0 -1.783 6.622 0.035
57 H26 H H26 N N N 0 -3.711 6.717 -1.48
58 H27 H H27 N N N 0 -5.113 4.73 -1.844
59 H28 H H28 N N N 0 -4.604 2.629 -0.704



5PS : Chemical Bonds

Total Number of Bonds: 63
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.38 N Y
2 C1 C5 C C doub 1.39 N Y
3 F1 C17 F C sing 1.35 N N
4 N1 C2 N C doub 1.32 N Y
5 N1 C3 N C sing 1.32 N Y
6 O1 C8 O C doub 1.22 N N
7 F2 C20 F C sing 1.35 N N
8 N2 C5 N C sing 1.4 N N
9 N2 C6 N C sing 1.35 N N
10 O2 C6 O C doub 1.21 N N
11 C3 C4 C C doub 1.38 N Y
12 N3 C8 N C sing 1.35 N N
13 N3 C7 N C sing 1.46 N N
14 C4 C5 C C sing 1.39 N Y
15 N4 C23 N C sing 1.37 N Y
16 N4 C24 N C sing 1.38 N Y
17 C6 C7 C C sing 1.51 N N
18 C8 C9 C C sing 1.47 N N
19 C9 C10 C C doub 1.4 N Y
20 C9 C20 C C sing 1.4 N Y
21 C10 C11 C C sing 1.38 N Y
22 C11 C12 C C doub 1.4 N Y
23 C12 C13 C C sing 1.48 N N
24 C12 C19 C C sing 1.39 N Y
25 C13 C14 C C sing 1.39 N Y
26 C13 C18 C C doub 1.39 N Y
27 C14 C15 C C doub 1.38 N Y
28 C15 C16 C C sing 1.38 N Y
29 C16 C17 C C doub 1.38 N Y
30 C17 C18 C C sing 1.38 N Y
31 C19 C20 C C doub 1.38 N Y
32 C21 C22 C C sing 1.51 N N
33 C21 C7 C C sing 1.53 N N
34 C22 C23 C C doub 1.34 N Y
35 C22 C29 C C sing 1.46 N Y
36 C24 C25 C C doub 1.39 N Y
37 C24 C29 C C sing 1.41 N Y
38 C25 C26 C C sing 1.38 N Y
39 C26 C27 C C doub 1.39 N Y
40 C27 C28 C C sing 1.37 N Y
41 C28 C29 C C doub 1.4 N Y
42 C1 H1 C H sing 1.08 N N
43 C2 H2 C H sing 1.08 N N
44 C3 H3 C H sing 1.08 N N
45 N2 HA N H sing 0.97 N N
46 C4 H4 C H sing 1.08 N N
47 N3 HB N H sing 0.97 N N
48 C7 H7 C H sing 1.09 N N
49 N4 HC N H sing 0.97 N N
50 C23 H23 C H sing 1.08 N N
51 C10 H10 C H sing 1.08 N N
52 C11 H11 C H sing 1.08 N N
53 C19 H19 C H sing 1.08 N N
54 C14 H14 C H sing 1.08 N N
55 C18 H18 C H sing 1.08 N N
56 C15 H15 C H sing 1.08 N N
57 C16 H16 C H sing 1.08 N N
58 C21 H211 C H sing 1.09 N N
59 C21 H212 C H sing 1.09 N N
60 C25 H25 C H sing 1.08 N N
61 C26 H26 C H sing 1.08 N N
62 C27 H27 C H sing 1.08 N N
63 C28 H28 C H sing 1.08 N N



5PS : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
5PS 4by0 Open in New Window Bound ligand 2 1