Chemical Components in the PDB

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KAF : Summary

Code

KAF

One-letter code

X

Molecule name

N-{(5S)-4,4-dihydroxy-6-phenyl-5-[(phenylcarbonyl)amino]hexanoyl}-L-phenylalanine

Systematic names

ProgramVersionName
ACDLabs 10.04 N-{(5S)-4,4-dihydroxy-6-phenyl-5-[(phenylcarbonyl)amino]hexanoyl}-L-phenylalanine
OpenEye OEToolkits 1.5.0 (2S)-2-[[(5S)-5-benzamido-4,4-dihydroxy-6-phenyl-hexanoyl]amino]-3-phenyl-propanoic acid

Formula

C28 H30 N2 O6

Formal charge

0

Molecular weight

490.548 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(NC(=O)CCC(O)(O)C(NC(=O)c1ccccc1)Cc2ccccc2)Cc3ccccc3
SMILES CACTVS 3.341 OC(=O)[CH](Cc1ccccc1)NC(=O)CCC(O)(O)[CH](Cc2ccccc2)NC(=O)c3ccccc3
SMILES OpenEye OEToolkits 1.5.0 c1ccc(cc1)CC(C(=O)O)NC(=O)CCC(C(Cc2ccccc2)NC(=O)c3ccccc3)(O)O
Canonical SMILES CACTVS 3.341 OC(=O)[C@H](Cc1ccccc1)NC(=O)CCC(O)(O)[C@H](Cc2ccccc2)NC(=O)c3ccccc3
Canonical SMILES OpenEye OEToolkits 1.5.0 c1ccc(cc1)C[C@@H](C(=O)O)NC(=O)CCC([C@H](Cc2ccccc2)NC(=O)c3ccccc3)(O)O

IUPAC InChI

InChI=1S/C28H30N2O6/c31-25(29-23(27(33)34)18-20-10-4-1-5-11-20)16-17-28(35,36)24(19-21-12-6-2-7-13-21)30-26(32)22-14-8-3-9-15-22/h1-15,23-24,35-36H,16-19H2,(H,29,31)(H,30,32)(H,33,34)/t23-,24-/m0/s1

IUPAC InChI key

XSYPPQBCHNRTIT-ZEQRLZLVSA-N
KAF

wwPDB Information

Atom count

66 (36 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2007-12-18

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



KAF : 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 CD1 C CD1 N Y N 0 7.025 -0.569 -1.7
2 CE1 C CE1 N Y N 0 6.927 -0.533 -3.079
3 CZ C CZ N Y N 0 6.325 0.544 -3.701
4 CE2 C CE2 N Y N 0 5.821 1.586 -2.945
5 CD2 C CD2 N Y N 0 5.919 1.55 -1.566
6 CG C CG N Y N 0 6.516 0.47 -0.944
7 CB C CB N N N 0 6.623 0.43 0.559
8 CA C CA S N N 0 5.381 -0.247 1.141
9 C C C N N N 0 5.543 -0.397 2.632
10 O O O N N N 0 6.564 -1.112 3.128
11 OXT O OXT N N N 0 4.752 0.126 3.381
12 N N N N N N 0 4.2 0.572 0.858
13 CBC C CBC N N N 0 2.98 0.0 0.803
14 OAA O OAA N N N 0 2.861 -1.193 0.987
15 CAV C CAV N N N 0 1.765 0.842 0.511
16 CAW C CAW N N N 0 0.519 -0.045 0.505
17 CBM C CBM N N N 0 -0.715 0.811 0.209
18 OAE O OAE N N N 0 -0.85 1.815 1.217
19 OAF O OAF N N N 0 -0.567 1.433 -1.068
20 CBL C CBL S N N 0 -1.961 -0.077 0.204
21 CAX C CAX N N N 0 -1.872 -1.073 -0.954
22 CBF C CBF N Y N 0 -3.038 -2.026 -0.888
23 CAO C CAO N Y N 0 -2.93 -3.2 -0.166
24 CAI C CAI N Y N 0 -3.999 -4.074 -0.105
25 CAG C CAG N Y N 0 -5.176 -3.774 -0.765
26 CAJ C CAJ N Y N 0 -5.284 -2.599 -1.486
27 CAP C CAP N Y N 0 -4.216 -1.723 -1.543
28 NBA N NBA N N N 0 -3.154 0.758 0.039
29 CBE C CBE N N N 0 -4.347 0.324 0.491
30 OAC O OAC N N N 0 -4.434 -0.76 1.035
31 CBG C CBG N Y N 0 -5.551 1.166 0.325
32 CAR C CAR N Y N 0 -5.456 2.409 -0.304
33 CAQ C CAQ N Y N 0 -6.788 0.72 0.792
34 CAL C CAL N Y N 0 -6.583 3.19 -0.456
35 CAH C CAH N Y N 0 -7.806 2.744 0.014
36 CAK C CAK N Y N 0 -7.906 1.513 0.639
37 HD1 H HD1 N N N 0 7.496 -1.411 -1.214
38 HE1 H HE1 N N N 0 7.321 -1.347 -3.67
39 HZ H HZ N N N 0 6.248 0.572 -4.778
40 HE2 H HE2 N N N 0 5.351 2.428 -3.431
41 HD2 H HD2 N N N 0 5.525 2.364 -0.975
42 HB H HB N N N 0 7.512 -0.132 0.845
43 HBA H HBA N N N 0 6.696 1.447 0.945
44 HA H HA N N N 0 5.258 -1.231 0.688
45 HO H HO N N N 0 6.627 -1.18 4.09
46 HN H HN N N N 0 4.295 1.526 0.71
47 HAV H HAV N N N 0 1.662 1.609 1.279
48 HAVA H HAVA N N N 0 1.878 1.317 -0.463
49 HAW H HAW N N N 0 0.622 -0.811 -0.263
50 HAWA H HAWA N N N 0 0.407 -0.52 1.48
51 HOAE H HOAE N N N 0 -0.954 1.464 2.111
52 HOAF H HOAF N N N 0 -0.47 0.81 -1.801
53 HBL H HBL N N N 0 -2.025 -0.62 1.146
54 HAX H HAX N N N 0 -1.898 -0.533 -1.901
55 HAXA H HAXA N N N 0 -0.94 -1.633 -0.881
56 HAO H HAO N N N 0 -2.01 -3.435 0.349
57 HAI H HAI N N N 0 -3.915 -4.992 0.458
58 HAG H HAG N N N 0 -6.011 -4.457 -0.717
59 HAJ H HAJ N N N 0 -6.204 -2.365 -2.001
60 HAP H HAP N N N 0 -4.302 -0.803 -2.103
61 HNBA H HNBA N N N 0 -3.085 1.623 -0.395
62 HAR H HAR N N N 0 -4.502 2.758 -0.671
63 HAL H HAL N N N 0 -6.511 4.151 -0.942
64 HAH H HAH N N N 0 -8.685 3.359 -0.107
65 HAK H HAK N N N 0 -8.864 1.171 1.004
66 HAQ H HAQ N N N 0 -6.869 -0.242 1.276



KAF : Chemical Bonds

Total Number of Bonds: 68
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CE1 CD1 C C doub 1.38 N Y
2 CG CD1 C C sing 1.38 N Y
3 CD1 HD1 C H sing 1.08 N N
4 CZ CE1 C C sing 1.38 N Y
5 CE1 HE1 C H sing 1.08 N N
6 CE2 CZ C C doub 1.38 N Y
7 CZ HZ C H sing 1.08 N N
8 CE2 CD2 C C sing 1.38 N Y
9 CE2 HE2 C H sing 1.08 N N
10 CD2 CG C C doub 1.38 N Y
11 CD2 HD2 C H sing 1.08 N N
12 CG CB C C sing 1.51 N N
13 CB CA C C sing 1.53 N N
14 CB HB C H sing 1.09 N N
15 CB HBA C H sing 1.09 N N
16 C CA C C sing 1.51 N N
17 CA N C N sing 1.46 N N
18 CA HA C H sing 1.09 N N
19 OXT C O C doub 1.21 N N
20 C O C O sing 1.34 N N
21 O HO O H sing 0.97 N N
22 N CBC N C sing 1.35 N N
23 N HN N H sing 0.97 N N
24 CBC OAA C O doub 1.21 N N
25 CBC CAV C C sing 1.51 N N
26 CAV CAW C C sing 1.53 N N
27 CAV HAV C H sing 1.09 N N
28 CAV HAVA C H sing 1.09 N N
29 CAW CBM C C sing 1.53 N N
30 CAW HAW C H sing 1.09 N N
31 CAW HAWA C H sing 1.09 N N
32 OAE CBM O C sing 1.43 N N
33 CBM OAF C O sing 1.43 N N
34 CBM CBL C C sing 1.53 N N
35 OAE HOAE O H sing 0.97 N N
36 OAF HOAF O H sing 0.97 N N
37 CAX CBL C C sing 1.53 N N
38 CBL NBA C N sing 1.47 N N
39 CBL HBL C H sing 1.09 N N
40 CAX CBF C C sing 1.51 N N
41 CAX HAX C H sing 1.09 N N
42 CAX HAXA C H sing 1.09 N N
43 CBF CAP C C doub 1.38 N Y
44 CBF CAO C C sing 1.38 N Y
45 CAO CAI C C doub 1.38 N Y
46 CAO HAO C H sing 1.08 N N
47 CAI CAG C C sing 1.38 N Y
48 CAI HAI C H sing 1.08 N N
49 CAJ CAG C C doub 1.38 N Y
50 CAG HAG C H sing 1.08 N N
51 CAP CAJ C C sing 1.38 N Y
52 CAJ HAJ C H sing 1.08 N N
53 CAP HAP C H sing 1.08 N N
54 NBA CBE N C sing 1.35 N N
55 NBA HNBA N H sing 0.97 N N
56 CBE OAC C O doub 1.22 N N
57 CBE CBG C C sing 1.48 N N
58 CAR CBG C C doub 1.4 N Y
59 CBG CAQ C C sing 1.4 N Y
60 CAR CAL C C sing 1.38 N Y
61 CAR HAR C H sing 1.08 N N
62 CAL CAH C C doub 1.38 N Y
63 CAL HAL C H sing 1.08 N N
64 CAH CAK C C sing 1.38 N Y
65 CAH HAH C H sing 1.08 N N
66 CAQ CAK C C doub 1.38 N Y
67 CAK HAK C H sing 1.08 N N
68 CAQ HAQ C H sing 1.08 N N



KAF : Used in PDB Entries

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