Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

3DZ : Summary

Code

3DZ

One-letter code

X

Molecule name

(2S)-2-[3-(aminomethyl)benzyl]-3-[(R)-[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]propanoic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S)-2-[3-(aminomethyl)benzyl]-3-[(R)-[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]propanoic acid
OpenEye OEToolkits 1.7.6 (2S)-2-[[3-(aminomethyl)phenyl]methyl]-3-[[(1R)-1-azanyl-3-phenyl-propyl]-oxidanyl-phosphoryl]propanoic acid

Formula

C20 H27 N2 O4 P

Formal charge

0

Molecular weight

390.413 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C(Cc1cccc(c1)CN)CP(=O)(O)C(N)CCc2ccccc2
SMILES CACTVS 3.385 NCc1cccc(C[CH](C[P](O)(=O)[CH](N)CCc2ccccc2)C(O)=O)c1
SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)CCC(N)P(=O)(CC(Cc2cccc(c2)CN)C(=O)O)O
Canonical SMILES CACTVS 3.385 NCc1cccc(C[C@H](C[P](O)(=O)[C@@H](N)CCc2ccccc2)C(O)=O)c1
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)CC[C@H](N)P(=O)(C[C@@H](Cc2cccc(c2)CN)C(=O)O)O

IUPAC InChI

InChI=1S/C20H27N2O4P/c21-13-17-8-4-7-16(11-17)12-18(20(23)24)14-27(25,26)19(22)10-9-15-5-2-1-3-6-15/h1-8,11,18-19H,9-10,12-14,21-22H2,(H,23,24)(H,25,26)/t18-,19-/m1/s1

IUPAC InChI key

OGZYJUYHRXGJNP-RTBURBONSA-N
3DZ

wwPDB Information

Atom count

54 (27 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-08-01

Last modified at

2014-09-05

Status

Released

Obsoleted

Not Assigned



3DZ : Atoms of Molecule

Total Number of Atoms: 54
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OAA O OAA N N N 0 -2.732 0.999 1.361
2 CAB C CAB N N N 0 -1.729 0.659 0.78
3 OAC O OAC N N N 0 -0.689 1.503 0.685
4 CAD C CAD S N N 0 -1.642 -0.716 0.168
5 CAE C CAE N N N 0 -2.948 -1.471 0.423
6 CAF C CAF N Y N 0 -4.076 -0.782 -0.3
7 CAK C CAK N Y N 0 -4.39 -1.145 -1.596
8 CAJ C CAJ N Y N 0 -5.425 -0.514 -2.26
9 CAI C CAI N Y N 0 -6.147 0.481 -1.627
10 CAH C CAH N Y N 0 -5.834 0.844 -0.33
11 CAZ C CAZ N N N 0 -6.62 1.928 0.36
12 NBA N NBA N N N 0 -7.763 1.332 1.064
13 CAG C CAG N Y N 0 -4.802 0.209 0.335
14 CAL C CAL N N N 0 -0.478 -1.482 0.797
15 PAM P PAM N N N 0 1.097 -0.849 0.133
16 OAN O OAN N N N 0 1.074 -0.922 -1.345
17 OAO O OAO N N N 0 1.297 0.681 0.592
18 CAP C CAP R N N 0 2.475 -1.859 0.769
19 NAQ N NAQ N N N 0 2.293 -3.255 0.35
20 CAR C CAR N N N 0 3.797 -1.328 0.211
21 CAS C CAS N N N 0 3.987 0.126 0.647
22 CAT C CAT N Y N 0 5.289 0.65 0.097
23 CAU C CAU N Y N 0 6.453 0.515 0.831
24 CAY C CAY N Y N 0 5.32 1.26 -1.142
25 CAX C CAX N Y N 0 6.514 1.74 -1.647
26 CAW C CAW N Y N 0 7.677 1.61 -0.911
27 CAV C CAV N Y N 0 7.647 0.995 0.327
28 H1 H H1 N N N 0 -0.79 2.372 1.097
29 H2 H H2 N N N 0 -1.479 -0.625 -0.906
30 H3 H H3 N N N 0 -2.853 -2.494 0.058
31 H4 H H4 N N N 0 -3.156 -1.484 1.493
32 H5 H H5 N N N 0 -3.826 -1.922 -2.091
33 H6 H H6 N N N 0 -5.67 -0.797 -3.273
34 H7 H H7 N N N 0 -6.956 0.975 -2.145
35 H8 H H8 N N N 0 -5.98 2.441 1.077
36 H9 H H9 N N N 0 -6.982 2.642 -0.38
37 H10 H H10 N N N 0 -7.458 0.62 1.711
38 H11 H H11 N N N 0 -8.307 2.039 1.535
39 H13 H H13 N N N 0 -4.56 0.489 1.349
40 H14 H H14 N N N 0 -0.496 -1.347 1.879
41 H15 H H15 N N N 0 -0.571 -2.543 0.562
42 H16 H H16 N N N 0 1.322 0.804 1.551
43 H17 H H17 N N N 0 2.493 -1.806 1.857
44 H18 H H18 N N N 0 1.459 -3.65 0.758
45 H19 H H19 N N N 0 2.274 -3.331 -0.656
46 H21 H H21 N N N 0 4.621 -1.932 0.591
47 H22 H H22 N N N 0 3.78 -1.381 -0.878
48 H23 H H23 N N N 0 3.163 0.73 0.267
49 H24 H H24 N N N 0 4.004 0.18 1.736
50 H25 H H25 N N N 0 6.429 0.034 1.798
51 H26 H H26 N N N 0 4.411 1.362 -1.717
52 H27 H H27 N N N 0 6.539 2.217 -2.615
53 H28 H H28 N N N 0 8.611 1.984 -1.305
54 H29 H H29 N N N 0 8.556 0.89 0.9



3DZ : Chemical Bonds

Total Number of Bonds: 55
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAN PAM O P doub 1.48 N N
2 CAE CAF C C sing 1.51 N N
3 CAE CAD C C sing 1.53 N N
4 CAP PAM C P sing 1.82 N N
5 CAP NAQ C N sing 1.47 N N
6 CAP CAR C C sing 1.53 N N
7 CAL PAM C P sing 1.82 N N
8 CAL CAD C C sing 1.53 N N
9 PAM OAO P O sing 1.61 N N
10 CAU CAV C C doub 1.38 N Y
11 CAU CAT C C sing 1.38 N Y
12 CAV CAW C C sing 1.38 N Y
13 CAF CAK C C doub 1.38 N Y
14 CAF CAG C C sing 1.38 N Y
15 CAK CAJ C C sing 1.38 N Y
16 CAG CAH C C doub 1.38 N Y
17 CAJ CAI C C doub 1.38 N Y
18 CAH CAI C C sing 1.38 N Y
19 CAH CAZ C C sing 1.51 N N
20 CAD CAB C C sing 1.51 N N
21 CAZ NBA C N sing 1.47 N N
22 CAS CAR C C sing 1.53 N N
23 CAS CAT C C sing 1.51 N N
24 CAT CAY C C doub 1.38 N Y
25 CAW CAX C C doub 1.38 N Y
26 OAA CAB O C doub 1.21 N N
27 CAB OAC C O sing 1.34 N N
28 CAX CAY C C sing 1.38 N Y
29 OAC H1 O H sing 0.97 N N
30 CAD H2 C H sing 1.09 N N
31 CAE H3 C H sing 1.09 N N
32 CAE H4 C H sing 1.09 N N
33 CAK H5 C H sing 1.08 N N
34 CAJ H6 C H sing 1.08 N N
35 CAI H7 C H sing 1.08 N N
36 CAZ H8 C H sing 1.09 N N
37 CAZ H9 C H sing 1.09 N N
38 NBA H10 N H sing 1.01 N N
39 NBA H11 N H sing 1.01 N N
40 CAG H13 C H sing 1.08 N N
41 CAL H14 C H sing 1.09 N N
42 CAL H15 C H sing 1.09 N N
43 OAO H16 O H sing 0.97 N N
44 CAP H17 C H sing 1.09 N N
45 NAQ H18 N H sing 1.01 N N
46 NAQ H19 N H sing 1.01 N N
47 CAR H21 C H sing 1.09 N N
48 CAR H22 C H sing 1.09 N N
49 CAS H23 C H sing 1.09 N N
50 CAS H24 C H sing 1.09 N N
51 CAU H25 C H sing 1.08 N N
52 CAY H26 C H sing 1.08 N N
53 CAX H27 C H sing 1.08 N N
54 CAW H28 C H sing 1.08 N N
55 CAV H29 C H sing 1.08 N N



3DZ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
3DZ 4quo Open in New Window Bound ligand 2 1