Chemical Components in the PDB

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25S : Summary

Code

25S

One-letter code

X

Molecule name

(R)-N-(3-(1H-indol-3-yl)-1-oxo-1-(pyridin-4-ylamino)propan-2-yl)-4-(4-(3,4-difluorophenyl)piperazin-1-yl)-2-fluorobenzamide

Systematic names

ProgramVersionName
ACDLabs 12.01 Nalpha-{4-[4-(3,4-difluorophenyl)piperazin-1-yl]-2-fluorobenzoyl}-N-pyridin-4-yl-D-tryptophanamide
OpenEye OEToolkits 1.7.6 4-[4-[3,4-bis(fluoranyl)phenyl]piperazin-1-yl]-2-fluoranyl-N-[(2R)-3-(1H-indol-3-yl)-1-oxidanylidene-1-(pyridin-4-ylamino)propan-2-yl]benzamide

Formula

C33 H29 F3 N6 O2

Formal charge

0

Molecular weight

598.618 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(Nc1ccncc1)C(NC(=O)c4ccc(N3CCN(c2cc(F)c(F)cc2)CC3)cc4F)Cc6c5ccccc5nc6
SMILES CACTVS 3.385 Fc1ccc(cc1F)N2CCN(CC2)c3ccc(C(=O)N[CH](Cc4c[nH]c5ccccc45)C(=O)Nc6ccncc6)c(F)c3
SMILES OpenEye OEToolkits 1.7.6 c1ccc2c(c1)c(c[nH]2)CC(C(=O)Nc3ccncc3)NC(=O)c4ccc(cc4F)N5CCN(CC5)c6ccc(c(c6)F)F
Canonical SMILES CACTVS 3.385 Fc1ccc(cc1F)N2CCN(CC2)c3ccc(C(=O)N[C@H](Cc4c[nH]c5ccccc45)C(=O)Nc6ccncc6)c(F)c3
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc2c(c1)c(c[nH]2)C[C@H](C(=O)Nc3ccncc3)NC(=O)c4ccc(cc4F)N5CCN(CC5)c6ccc(c(c6)F)F

IUPAC InChI

InChI=1S/C33H29F3N6O2/c34-27-8-6-24(19-29(27)36)42-15-13-41(14-16-42)23-5-7-26(28(35)18-23)32(43)40-31(33(44)39-22-9-11-37-12-10-22)17-21-20-38-30-4-2-1-3-25(21)30/h1-12,18-20,31,38H,13-17H2,(H,40,43)(H,37,39,44)/t31-/m1/s1

IUPAC InChI key

UJJHTUJDTNONGY-WJOKGBTCSA-N
25S

wwPDB Information

Atom count

73 (44 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-06-23

Last modified at

2014-08-15

Status

Released

Obsoleted

Not Assigned



25S : 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 O1 O O1 N N N 0 4.12 -2.271 -0.472
2 C5 C C5 N N N 0 4.835 -1.298 -0.359
3 N1 N N1 N N N 0 6.174 -1.446 -0.324
4 C4 C C4 N Y N 0 6.735 -2.724 -0.305
5 C3 C C3 N Y N 0 7.964 -2.975 -0.914
6 C2 C C2 N Y N 0 8.484 -4.252 -0.873
7 N N N N Y N 0 7.833 -5.228 -0.269
8 C1 C C1 N Y N 0 6.668 -5.031 0.319
9 C C C N Y N 0 6.083 -3.782 0.327
10 C6 C C6 R N N 0 4.226 0.077 -0.266
11 C24 C C24 N N N 0 4.73 0.938 -1.427
12 C25 C C25 N Y N 0 4.219 2.346 -1.266
13 C28 C C28 N Y N 0 4.833 3.41 -0.468
14 C29 C C29 N Y N 0 5.974 3.486 0.333
15 C30 C C30 N Y N 0 6.283 4.658 0.964
16 C31 C C31 N Y N 0 5.471 5.774 0.815
17 C32 C C32 N Y N 0 4.341 5.721 0.03
18 C27 C C27 N Y N 0 4.007 4.538 -0.622
19 N5 N N5 N Y N 0 2.973 4.173 -1.454
20 C26 C C26 N Y N 0 3.119 2.866 -1.833
21 N2 N N2 N N N 0 2.767 -0.029 -0.334
22 C7 C C7 N N N 0 2.056 -0.278 0.784
23 O O O N N N 0 2.627 -0.415 1.849
24 C8 C C8 N Y N 0 0.588 -0.385 0.715
25 C23 C C23 N Y N 0 -0.152 -0.644 1.876
26 F2 F F2 N N N 0 0.477 -0.797 3.062
27 C22 C C22 N Y N 0 -1.526 -0.743 1.804
28 C11 C C11 N Y N 0 -2.17 -0.584 0.58
29 C10 C C10 N Y N 0 -1.431 -0.328 -0.572
30 C9 C C9 N Y N 0 -0.07 -0.223 -0.507
31 N3 N N3 N N N 0 -3.555 -0.683 0.507
32 C21 C C21 N N N 0 -4.025 -0.485 -0.871
33 C20 C C20 N N N 0 -5.542 -0.68 -0.922
34 N4 N N4 N N N 0 -6.187 0.271 -0.006
35 C13 C C13 N N N 0 -5.717 0.072 1.372
36 C12 C C12 N N N 0 -4.2 0.268 1.423
37 C14 C C14 N Y N 0 -7.58 0.172 -0.079
38 C19 C C19 N Y N 0 -8.378 0.989 0.711
39 C18 C C18 N Y N 0 -9.754 0.889 0.638
40 C17 C C17 N Y N 0 -10.339 -0.024 -0.222
41 F1 F F1 N N N 0 -11.685 -0.119 -0.291
42 C16 C C16 N Y N 0 -9.545 -0.841 -1.013
43 F F F N N N 0 -10.118 -1.731 -1.852
44 C15 C C15 N Y N 0 -8.167 -0.74 -0.946
45 H1 H H1 N N N 0 6.748 -0.664 -0.311
46 H6 H H6 N N N 0 4.513 0.538 0.679
47 H3 H H3 N N N 0 8.501 -2.18 -1.411
48 H H H N N N 0 5.132 -3.626 0.814
49 H2 H H2 N N N 0 9.435 -4.455 -1.342
50 HA H HA N N N 0 6.168 -5.857 0.803
51 H241 H H241 N N N 0 5.82 0.944 -1.429
52 H242 H H242 N N N 0 4.367 0.525 -2.369
53 HB H HB N N N 0 2.312 0.08 -1.184
54 H26 H H26 N N N 0 2.447 2.332 -2.488
55 H29 H H29 N N N 0 6.61 2.622 0.454
56 H30 H H30 N N N 0 7.166 4.716 1.584
57 H31 H H31 N N N 0 5.728 6.694 1.32
58 H32 H H32 N N N 0 3.716 6.595 -0.08
59 H5 H H5 N N N 0 2.251 4.757 -1.734
60 H9 H H9 N N N 0 0.498 -0.019 -1.403
61 H22 H H22 N N N 0 -2.102 -0.942 2.695
62 H10 H H10 N N N 0 -1.935 -0.206 -1.519
63 H211 H H211 N N N 0 -3.777 0.525 -1.197
64 H212 H H212 N N N 0 -3.543 -1.209 -1.527
65 H121 H H121 N N N 0 -3.845 0.092 2.439
66 H122 H H122 N N N 0 -3.954 1.286 1.123
67 H201 H H201 N N N 0 -5.898 -0.504 -1.937
68 H202 H H202 N N N 0 -5.788 -1.698 -0.621
69 H131 H H131 N N N 0 -6.199 0.797 2.029
70 H132 H H132 N N N 0 -5.965 -0.937 1.699
71 H19 H H19 N N N 0 -7.923 1.701 1.383
72 H15 H H15 N N N 0 -7.548 -1.373 -1.565
73 H18 H H18 N N N 0 -10.374 1.525 1.253



25S : Chemical Bonds

Total Number of Bonds: 78
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1 C5 O C doub 1.21 N N
2 C5 N1 C N sing 1.35 N N
3 C5 C6 C C sing 1.51 N N
4 N1 C4 N C sing 1.4 N N
5 C4 C3 C C doub 1.39 N Y
6 C4 C C C sing 1.39 N Y
7 C3 C2 C C sing 1.38 N Y
8 C2 N C N doub 1.32 N Y
9 N C1 N C sing 1.32 N Y
10 C1 C C C doub 1.38 N Y
11 C6 C24 C C sing 1.53 N N
12 C6 N2 C N sing 1.46 N N
13 C24 C25 C C sing 1.51 N N
14 C25 C28 C C sing 1.46 N Y
15 C25 C26 C C doub 1.34 N Y
16 C28 C29 C C sing 1.4 N Y
17 C28 C27 C C doub 1.41 N Y
18 C29 C30 C C doub 1.37 N Y
19 C30 C31 C C sing 1.39 N Y
20 C31 C32 C C doub 1.38 N Y
21 C32 C27 C C sing 1.39 N Y
22 C27 N5 C N sing 1.38 N Y
23 N5 C26 N C sing 1.37 N Y
24 N2 C7 N C sing 1.35 N N
25 C7 O C O doub 1.22 N N
26 C7 C8 C C sing 1.47 N N
27 C8 C23 C C sing 1.4 N Y
28 C8 C9 C C doub 1.4 N Y
29 C23 F2 C F sing 1.35 N N
30 C23 C22 C C doub 1.38 N Y
31 C22 C11 C C sing 1.39 N Y
32 C11 C10 C C doub 1.39 N Y
33 C11 N3 C N sing 1.39 N N
34 C10 C9 C C sing 1.37 N Y
35 N3 C21 N C sing 1.47 N N
36 N3 C12 N C sing 1.47 N N
37 C21 C20 C C sing 1.53 N N
38 C20 N4 C N sing 1.47 N N
39 N4 C13 N C sing 1.47 N N
40 N4 C14 N C sing 1.4 N N
41 C13 C12 C C sing 1.53 N N
42 C14 C19 C C sing 1.39 N Y
43 C14 C15 C C doub 1.39 N Y
44 C19 C18 C C doub 1.38 N Y
45 C18 C17 C C sing 1.38 N Y
46 C17 F1 C F sing 1.35 N N
47 C17 C16 C C doub 1.39 N Y
48 C16 F C F sing 1.35 N N
49 C16 C15 C C sing 1.38 N Y
50 N1 H1 N H sing 0.97 N N
51 C6 H6 C H sing 1.09 N N
52 C3 H3 C H sing 1.08 N N
53 C H C H sing 1.08 N N
54 C2 H2 C H sing 1.08 N N
55 C1 HA C H sing 1.08 N N
56 C24 H241 C H sing 1.09 N N
57 C24 H242 C H sing 1.09 N N
58 N2 HB N H sing 0.97 N N
59 C26 H26 C H sing 1.08 N N
60 C29 H29 C H sing 1.08 N N
61 C30 H30 C H sing 1.08 N N
62 C31 H31 C H sing 1.08 N N
63 C32 H32 C H sing 1.08 N N
64 N5 H5 N H sing 0.97 N N
65 C9 H9 C H sing 1.08 N N
66 C22 H22 C H sing 1.08 N N
67 C10 H10 C H sing 1.08 N N
68 C21 H211 C H sing 1.09 N N
69 C21 H212 C H sing 1.09 N N
70 C12 H121 C H sing 1.09 N N
71 C12 H122 C H sing 1.09 N N
72 C20 H201 C H sing 1.09 N N
73 C20 H202 C H sing 1.09 N N
74 C13 H131 C H sing 1.09 N N
75 C13 H132 C H sing 1.09 N N
76 C19 H19 C H sing 1.08 N N
77 C15 H15 C H sing 1.08 N N
78 C18 H18 C H sing 1.08 N N



25S : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
25S 4uqh Open in New Window Bound ligand 1 1