Chemical Components in the PDB

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DP7 : Summary

Code

DP7

One-letter code

X

Molecule name

AC-(D)PHE-PRO-BOROARG-OH

Systematic names

ProgramVersionName
ACDLabs 10.04 N-acetyl-D-phenylalanyl-N-[(1R)-4-carbamimidamido-1-(dihydroxyboranyl)butyl]-L-prolinamide
OpenEye OEToolkits 1.5.0 [(1R)-1-[[(2S)-1-[(2R)-2-acetamido-3-phenyl-propanoyl]pyrrolidin-2-yl]carbonylamino]-4-carbamimidamido-butyl]boronic acid

Formula

C21 H33 B N6 O5

Formal charge

0

Molecular weight

460.335 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(NC(B(O)O)CCCNC(=[N@H])N)C2N(C(=O)C(NC(=O)C)Cc1ccccc1)CCC2
SMILES CACTVS 3.341 CC(=O)N[CH](Cc1ccccc1)C(=O)N2CCC[CH]2C(=O)N[CH](CCCNC(N)=N)B(O)O
SMILES OpenEye OEToolkits 1.5.0 [H]N=C(N)NCCCC(B(O)O)NC(=O)C1CCCN1C(=O)C(Cc2ccccc2)NC(=O)C
Canonical SMILES CACTVS 3.341 CC(=O)N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)N[C@@H](CCCNC(N)=N)B(O)O
Canonical SMILES OpenEye OEToolkits 1.5.0 [H]/N=C(/N)\NCCC[C@@H](B(O)O)NC(=O)[C@@H]1CCCN1C(=O)[C@@H](Cc2ccccc2)NC(=O)C

IUPAC InChI

InChI=1S/C21H33BN6O5/c1-14(29)26-16(13-15-7-3-2-4-8-15)20(31)28-12-6-9-17(28)19(30)27-18(22(32)33)10-5-11-25-21(23)24/h2-4,7-8,16-18,32-33H,5-6,9-13H2,1H3,(H,26,29)(H,27,30)(H4,23,24,25)/t16-,17+,18+/m1/s1

IUPAC InChI key

FXFYPTZERULUBS-SQNIBIBYSA-N
DP7

wwPDB Information

Atom count

66 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



DP7 : Atoms of Molecule

Total Number of Atoms: 66
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 R N N 0 -0.588 0.287 -3.111
2 B2 B B2 N N N 0 -1.566 1.444 -3.523
3 C3 C C3 N N N 0 -0.291 -0.588 -4.33
4 C4 C C4 N N N 0 0.357 0.263 -5.423
5 C5 C C5 N N N 0 0.655 -0.612 -6.642
6 C6 C C6 N N N 0 1.634 -0.371 -8.886
7 C7 C C7 S N N 0 -1.663 -1.051 0.309
8 C8 C C8 N N N 0 -1.024 -0.213 -0.767
9 C9 C C9 N N N 0 -3.199 -1.007 0.167
10 C10 C C10 N N N 0 -3.686 -0.966 1.639
11 C11 C C11 N N N 0 -2.582 -0.109 2.308
12 C12 C C12 N N N 0 -0.093 -0.404 2.154
13 C13 C C13 N N N 0 0.044 -0.95 4.569
14 C14 C C14 R N N 0 0.1 0.173 3.532
15 C15 C C15 N N N 0 2.531 0.138 3.384
16 C16 C C16 N N N 0 3.871 0.824 3.457
17 C17 C C17 N Y N 0 1.687 0.27 7.742
18 C18 C C18 N Y N 0 0.592 0.688 8.476
19 C19 C C19 N Y N 0 -0.678 0.576 7.946
20 C20 C C20 N Y N 0 -0.856 0.045 6.682
21 C21 C C21 N Y N 0 0.238 -0.371 5.947
22 C22 C C22 N Y N 0 1.509 -0.264 6.48
23 N1 N N1 N N N 0 -1.209 -0.527 -2.064
24 N2 N N2 N N N 0 1.276 0.202 -7.689
25 N3 N N3 N N N 0 2.217 0.393 -9.868
26 N4 N N4 N N N 0 1.421 -1.641 -9.089
27 N5 N N5 N N N 0 -1.333 -0.514 1.637
28 N6 N N6 N N N 0 1.402 0.84 3.604
29 O1 O O1 N N N 0 -2.85 1.135 -4.045
30 O2 O O2 N N N 0 -1.167 2.798 -3.374
31 O3 O O3 N N N 0 -0.343 0.744 -0.466
32 O4 O O4 N N N 0 0.866 -0.771 1.51
33 O5 O O5 N N N 0 2.469 -1.045 3.127
34 H41 H 1H4 N N N 0 -0.321 1.066 -5.71
35 H1 H H1 N N N 0 0.341 0.714 -2.735
36 H31 H 1H3 N N N 0 0.388 -1.391 -4.044
37 H32 H 2H3 N N N 0 -1.22 -1.015 -4.706
38 H42 H 2H4 N N N 0 1.287 0.69 -5.047
39 H51 H 1H5 N N N 0 1.334 -1.415 -6.356
40 H52 H 2H5 N N N 0 -0.274 -1.039 -7.018
41 H7 H H7 N N N 0 -1.313 -2.081 0.234
42 H91 H 1H9 N N N 0 -3.568 -1.902 -0.335
43 H92 H 2H9 N N N 0 -3.508 -0.109 -0.366
44 H101 H 1H10 N N N 0 -3.718 -1.967 2.069
45 H102 H 2H10 N N N 0 -4.658 -0.478 1.715
46 H111 H 1H11 N N N 0 -2.528 -0.326 3.374
47 H112 H 2H11 N N N 0 -2.774 0.951 2.144
48 H131 H 1H13 N N N 0 -0.924 -1.446 4.516
49 H132 H 2H13 N N N 0 0.834 -1.672 4.364
50 H14 H H14 N N N 0 -0.689 0.896 3.737
51 H161 H 1H16 N N N 0 4.661 0.101 3.253
52 H162 H 2H16 N N N 0 3.911 1.624 2.719
53 H163 H 3H16 N N N 0 4.011 1.242 4.454
54 H17 H H17 N N N 0 2.68 0.358 8.156
55 H18 H H18 N N N 0 0.731 1.103 9.463
56 H19 H H19 N N N 0 -1.533 0.903 8.519
57 H20 H H20 N N N 0 -1.849 -0.041 6.267
58 H22 H H22 N N N 0 2.364 -0.591 5.906
59 HN1 H HN1 N N N 0 -1.754 -1.293 -2.305
60 HN2 H HN2 N N N 0 1.434 1.147 -7.538
61 HN31 H 1HN3 N N N 0 2.47 -0.012 -10.712
62 HN32 H 2HN3 N N N 0 2.376 1.337 -9.717
63 HN4 H HN4 N N N 0 1.674 -2.047 -9.933
64 HN6 H HN6 N N N 0 1.452 1.787 3.81
65 HO1 H HO1 N N N 0 -3.285 1.978 -4.232
66 HO2 H HO2 N N N 0 -0.272 2.787 -3.008



DP7 : Chemical Bonds

Total Number of Bonds: 67
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 B2 C B sing 1.57 N N
2 C1 C3 C C sing 1.53 N N
3 C1 N1 C N sing 1.46 N N
4 C1 H1 C H sing 1.09 N N
5 B2 O1 B O sing 1.42 N N
6 B2 O2 B O sing 1.42 N N
7 C3 C4 C C sing 1.53 N N
8 C3 H31 C H sing 1.09 N N
9 C3 H32 C H sing 1.09 N N
10 C4 C5 C C sing 1.53 N N
11 C4 H41 C H sing 1.09 N N
12 C4 H42 C H sing 1.09 N N
13 C5 N2 C N sing 1.46 N N
14 C5 H51 C H sing 1.09 N N
15 C5 H52 C H sing 1.09 N N
16 C6 N2 C N sing 1.37 N N
17 C6 N3 C N sing 1.37 N N
18 C6 N4 C N doub 1.3 Z N
19 C7 C8 C C sing 1.51 N N
20 C7 C9 C C sing 1.54 N N
21 C7 N5 C N sing 1.47 N N
22 C7 H7 C H sing 1.09 N N
23 C8 N1 C N sing 1.35 N N
24 C8 O3 C O doub 1.21 N N
25 C9 C10 C C sing 1.55 N N
26 C9 H91 C H sing 1.09 N N
27 C9 H92 C H sing 1.09 N N
28 C10 C11 C C sing 1.55 N N
29 C10 H101 C H sing 1.09 N N
30 C10 H102 C H sing 1.09 N N
31 C11 N5 C N sing 1.47 N N
32 C11 H111 C H sing 1.09 N N
33 C11 H112 C H sing 1.09 N N
34 C12 C14 C C sing 1.51 N N
35 C12 N5 C N sing 1.35 N N
36 C12 O4 C O doub 1.21 N N
37 C13 C14 C C sing 1.53 N N
38 C13 C21 C C sing 1.51 N N
39 C13 H131 C H sing 1.09 N N
40 C13 H132 C H sing 1.09 N N
41 C14 N6 C N sing 1.46 N N
42 C14 H14 C H sing 1.09 N N
43 C15 C16 C C sing 1.51 N N
44 C15 N6 C N sing 1.35 N N
45 C15 O5 C O doub 1.21 N N
46 C16 H161 C H sing 1.09 N N
47 C16 H162 C H sing 1.09 N N
48 C16 H163 C H sing 1.09 N N
49 C17 C18 C C doub 1.38 N Y
50 C17 C22 C C sing 1.38 N Y
51 C17 H17 C H sing 1.08 N N
52 C18 C19 C C sing 1.38 N Y
53 C18 H18 C H sing 1.08 N N
54 C19 C20 C C doub 1.38 N Y
55 C19 H19 C H sing 1.08 N N
56 C20 C21 C C sing 1.38 N Y
57 C20 H20 C H sing 1.08 N N
58 C21 C22 C C doub 1.38 N Y
59 C22 H22 C H sing 1.08 N N
60 N1 HN1 N H sing 0.97 N N
61 N2 HN2 N H sing 0.97 N N
62 N3 HN31 N H sing 0.97 N N
63 N3 HN32 N H sing 0.97 N N
64 N4 HN4 N H sing 0.97 N N
65 N6 HN6 N H sing 0.97 N N
66 O1 HO1 O H sing 0.97 N N
67 O2 HO2 O H sing 0.97 N N



DP7 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
DP7 1lhc Open in New Window Bound ligand 1 1