Chemical Components in the PDB

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BD3 : Summary

Code

BD3

One-letter code

X

Molecule name

Nalpha-[(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)carbonyl]-N-[(2E)-2-iminoethyl]-3-{5-[(Z)-iminomethyl]-1,3,4-oxadiazol-2-yl}-L-phenylalaninamide

Systematic names

ProgramVersionName
ACDLabs 10.04 Nalpha-[(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)carbonyl]-N-[(2E)-2-iminoethyl]-3-{5-[(Z)-iminomethyl]-1,3,4-oxadiazol-2-yl}-L-phenylalaninamide
OpenEye OEToolkits 1.5.0 5-tert-butyl-N-[(2S)-1-(2-iminoethylamino)-3-[3-[5-(iminomethyl)-1,3,4-oxadiazol-2-yl]phenyl]-1-oxo-propan-2-yl]-2-methyl-pyrazole-3-carboxamide

Formula

C23 H28 N8 O3

Formal charge

0

Molecular weight

464.52 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(NCC=[N@H])C(NC(=O)c1cc(nn1C)C(C)(C)C)Cc3cc(c2nnc(o2)C=[N@H])ccc3
SMILES CACTVS 3.341 Cn1nc(cc1C(=O)N[CH](Cc2cccc(c2)c3oc(C=N)nn3)C(=O)NCC=N)C(C)(C)C
SMILES OpenEye OEToolkits 1.5.0 [H]N=CCNC(=O)C(Cc1cccc(c1)c2nnc(o2)C=N[H])NC(=O)c3cc(nn3C)C(C)(C)C
Canonical SMILES CACTVS 3.341 Cn1nc(cc1C(=O)N[C@@H](Cc2cccc(c2)c3oc(C=N)nn3)C(=O)NCC=N)C(C)(C)C
Canonical SMILES OpenEye OEToolkits 1.5.0 [H]/N=C/CNC(=O)[C@H](Cc1cccc(c1)c2nnc(o2)\C=N/[H])NC(=O)c3cc(nn3C)C(C)(C)C

IUPAC InChI

InChI=1S/C23H28N8O3/c1-23(2,3)18-12-17(31(4)30-18)21(33)27-16(20(32)26-9-8-24)11-14-6-5-7-15(10-14)22-29-28-19(13-25)34-22/h5-8,10,12-13,16,24-25H,9,11H2,1-4H3,(H,26,32)(H,27,33)/b24-8+,25-13-/t16-/m0/s1

IUPAC InChI key

TVWDSIGUOHNHHP-TTWIPJPDSA-N
BD3

wwPDB Information

Atom count

62 (34 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-06-19

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



BD3 : Atoms of Molecule

Total Number of Atoms: 62
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 -1.249 -2.445 -0.202
2 C2 C C2 N Y N 0 -1.463 -3.281 -1.283
3 C3 C C3 N Y N 0 0.033 -2.205 0.245
4 C4 C C4 N Y N 0 -0.394 -3.887 -1.92
5 C5 C C5 N Y N 0 1.117 -2.813 -0.392
6 C6 C C6 N Y N 0 0.893 -3.661 -1.479
7 C7 C C7 N Y N 0 2.493 -2.561 0.081
8 C12 C C12 N N N 0 6.07 -2.865 0.098
9 N13 N N13 N N N 0 6.95 -2.324 0.881
10 C15 C C15 S N N 0 -2.713 -0.443 -0.182
11 C17 C C17 N N N 0 -1.358 1.474 -0.831
12 C18 C C18 N Y N 0 -0.16 2.317 -0.682
13 N22 N N22 N N N 0 -5.128 -0.507 0.348
14 C23 C C23 N N N 0 -6.338 0.075 0.935
15 C24 C C24 N N N 0 -7.501 -0.857 0.716
16 C30 C C30 N N N 0 -0.413 3.691 -2.771
17 C31 C C31 N N N 0 2.924 3.603 0.859
18 C34 C C34 N N N 0 3.991 2.522 0.671
19 C32 C C32 N N N 0 2.539 3.687 2.337
20 C33 C C33 N N N 0 3.48 4.952 0.399
21 N25 N N25 N N N 0 -8.195 -1.259 1.713
22 C20 C C20 N N N 0 -3.957 0.155 0.423
23 O21 O O21 N N N 0 -3.904 1.233 0.976
24 N16 N N16 N N N 0 -1.582 0.463 0.031
25 O19 O O19 N N N 0 -2.145 1.691 -1.732
26 C29 C C29 N Y N 0 0.765 2.27 0.347
27 C28 C C28 N Y N 0 1.707 3.255 0.041
28 N27 N N27 N Y N 0 1.346 3.822 -1.081
29 N26 N N26 N Y N 0 0.264 3.297 -1.533
30 C14 C C14 N N N 0 -2.42 -1.789 0.484
31 O11 O O11 N Y N 0 3.622 -3.075 -0.442
32 C10 C C10 N Y N 0 4.641 -2.583 0.294
33 N9 N N9 N Y N 0 4.121 -1.805 1.219
34 N8 N N8 N Y N 0 2.841 -1.787 1.089
35 H2 H H2 N N N 0 -2.469 -3.463 -1.632
36 H3 H H3 N N N 0 0.199 -1.548 1.087
37 H4 H H4 N N N 0 -0.568 -4.539 -2.763
38 H6 H H6 N N N 0 1.727 -4.135 -1.976
39 H12 H H12 N N N 0 6.387 -3.522 -0.698
40 HN13 H HN13 N N N 0 6.666 -1.733 1.596
41 H15 H H15 N N N 0 -2.864 -0.592 -1.251
42 HN22 H HN22 N N N 0 -5.171 -1.369 -0.095
43 H23 H H23 N N N 0 -6.187 0.224 2.004
44 H23A H H23A N N N 0 -6.547 1.034 0.461
45 H24 H H24 N N N 0 -7.75 -1.186 -0.282
46 H30 H H30 N N N 0 -1.082 4.528 -2.568
47 H30A H H30A N N N 0 0.329 3.991 -3.511
48 H32A H H32A N N N 0 1.779 4.457 2.471
49 H30B H H30B N N N 0 -0.99 2.849 -3.154
50 H32 H H32 N N N 0 3.419 3.938 2.929
51 H32B H H32B N N N 0 2.143 2.726 2.665
52 H33 H H33 N N N 0 3.755 4.892 -0.654
53 H33A H H33A N N N 0 2.72 5.722 0.533
54 H33B H H33B N N N 0 4.36 5.203 0.991
55 H34 H H34 N N N 0 3.595 1.56 0.999
56 H34A H H34A N N N 0 4.266 2.461 -0.382
57 H34B H H34B N N N 0 4.871 2.773 1.263
58 HN25 H HN25 N N N 0 -8.944 -1.859 1.572
59 HN16 H HN16 N N N 0 -0.994 0.335 0.792
60 H29 H H29 N N N 0 0.759 1.613 1.204
61 H14 H H14 N N N 0 -3.296 -2.433 0.403
62 H14A H H14A N N N 0 -2.182 -1.631 1.536



BD3 : Chemical Bonds

Total Number of Bonds: 64
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C2 C1 C C doub 1.38 N Y
2 C1 C14 C C sing 1.51 N N
3 C1 C3 C C sing 1.38 N Y
4 C4 C2 C C sing 1.38 N Y
5 C2 H2 C H sing 1.08 N N
6 C5 C3 C C doub 1.4 N Y
7 C3 H3 C H sing 1.08 N N
8 C4 C6 C C doub 1.38 N Y
9 C4 H4 C H sing 1.08 N N
10 C6 C5 C C sing 1.4 N Y
11 C5 C7 C C sing 1.48 N Y
12 C6 H6 C H sing 1.08 N N
13 O11 C7 O C sing 1.35 N Y
14 C7 N8 C N doub 1.32 N Y
15 C12 N13 C N doub 1.3 N N
16 C12 C10 C C sing 1.47 N N
17 C12 H12 C H sing 1.08 N N
18 N13 HN13 N H sing 0.97 N N
19 C15 N16 C N sing 1.46 N N
20 C15 C14 C C sing 1.53 N N
21 C15 C20 C C sing 1.51 N N
22 C15 H15 C H sing 1.09 N N
23 O19 C17 O C doub 1.22 N N
24 C17 C18 C C sing 1.47 N N
25 C17 N16 C N sing 1.35 N N
26 N26 C18 N C sing 1.37 N Y
27 C18 C29 C C doub 1.38 N Y
28 N22 C20 N C sing 1.35 N N
29 N22 C23 N C sing 1.47 N N
30 N22 HN22 N H sing 0.97 N N
31 C23 C24 C C sing 1.51 N N
32 C23 H23 C H sing 1.09 N N
33 C23 H23A C H sing 1.09 N N
34 C24 N25 C N doub 1.28 N N
35 C24 H24 C H sing 1.08 N N
36 C30 N26 C N sing 1.46 N N
37 C30 H30 C H sing 1.09 N N
38 C30 H30A C H sing 1.09 N N
39 C30 H30B C H sing 1.09 N N
40 C28 C31 C C sing 1.51 N N
41 C33 C31 C C sing 1.53 N N
42 C31 C34 C C sing 1.53 N N
43 C31 C32 C C sing 1.53 N N
44 C32 H32 C H sing 1.09 N N
45 C32 H32A C H sing 1.09 N N
46 C32 H32B C H sing 1.09 N N
47 C33 H33 C H sing 1.09 N N
48 C33 H33A C H sing 1.09 N N
49 C33 H33B C H sing 1.09 N N
50 C34 H34 C H sing 1.09 N N
51 C34 H34A C H sing 1.09 N N
52 C34 H34B C H sing 1.09 N N
53 N25 HN25 N H sing 0.97 N N
54 C20 O21 C O doub 1.21 N N
55 N16 HN16 N H sing 0.97 N N
56 C28 C29 C C sing 1.4 N Y
57 C29 H29 C H sing 1.08 N N
58 N27 C28 N C doub 1.31 N Y
59 N26 N27 N N sing 1.28 N Y
60 C14 H14 C H sing 1.09 N N
61 C14 H14A C H sing 1.09 N N
62 O11 C10 O C sing 1.35 N Y
63 C10 N9 C N doub 1.32 N Y
64 N8 N9 N N sing 1.29 N Y



BD3 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
BD3 3hwn Open in New Window Bound ligand 4 1