Receptor
PDB id Resolution Class Description Source Keywords
2EFX 2.2 Å EC: 3.-.-.- THE CRYSTAL STRUCTURE OF D-AMINO ACID AMIDASE FROM OCHROBACTRUM ANTHROPI SV3 COMPLEXED WITH L-PHENYLALANINE A MIDE OCHROBACTRUM ANTHROPI PENICILLIN RECOGNIZING PROTEINS D-STEREOSPECIFIC AMIDASE L-PHENYLALANINE AMIDE HYDROLASE
Ref.: STRUCTURES OF D-AMINO-ACID AMIDASE COMPLEXED WITH L-PHENYLALANINE AND WITH L-PHENYLALANINE AMIDE: INSIGHT INTO THE D-STEREOSPECIFICITY OF D-AMINO-ACID AMIDASE FROM OCHROBACTRUM ANTHROPI SV3. ACTA CRYSTALLOGR.,SECT.D V. 64 331 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BA A:3003;
A:3004;
A:3008;
A:3017;
B:3002;
B:3007;
B:3009;
B:3021;
C:3001;
C:3005;
C:3010;
C:3012;
D:3013;
D:3015;
D:3016;
D:3020;
E:3011;
E:3014;
E:3019;
F:3006;
F:3018;
F:3022;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
137.327 Ba [Ba+2...
NFA A:2001;
B:2002;
C:2003;
D:2004;
E:2005;
F:2006;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
164.204 C9 H12 N2 O c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2EFX 2.2 Å EC: 3.-.-.- THE CRYSTAL STRUCTURE OF D-AMINO ACID AMIDASE FROM OCHROBACTRUM ANTHROPI SV3 COMPLEXED WITH L-PHENYLALANINE A MIDE OCHROBACTRUM ANTHROPI PENICILLIN RECOGNIZING PROTEINS D-STEREOSPECIFIC AMIDASE L-PHENYLALANINE AMIDE HYDROLASE
Ref.: STRUCTURES OF D-AMINO-ACID AMIDASE COMPLEXED WITH L-PHENYLALANINE AND WITH L-PHENYLALANINE AMIDE: INSIGHT INTO THE D-STEREOSPECIFICITY OF D-AMINO-ACID AMIDASE FROM OCHROBACTRUM ANTHROPI SV3. ACTA CRYSTALLOGR.,SECT.D V. 64 331 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 2EFU - PHE C9 H11 N O2 c1ccc(cc1)....
2 2EFX - NFA C9 H12 N2 O c1ccc(cc1)....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 176 families.
1 2EFU - PHE C9 H11 N O2 c1ccc(cc1)....
2 2EFX - NFA C9 H12 N2 O c1ccc(cc1)....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 143 families.
1 2EFU - PHE C9 H11 N O2 c1ccc(cc1)....
2 2EFX - NFA C9 H12 N2 O c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NFA; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 NFA 1 1
2 DPN 0.657143 0.666667
3 PHE 0.657143 0.666667
4 TYC 0.526316 0.766667
5 ING 0.431818 0.6
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2EFX; Ligand: NFA; Similar sites found: 6
This union binding pocket(no: 1) in the query (biounit: 2efx.bio4) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VGK REZ 0.001458 0.44648 1.92837
2 3ZOK NAD 0.04796 0.4028 3.58127
3 3G35 F13 0.02349 0.40645 4.56274
4 4OR7 NAP 0.002459 0.46669 8.48485
5 1YLH PYR 0.01497 0.40606 10.4683
6 2W9S NDP 0.008086 0.43742 14.2857
Pocket No.: 2; Query (leader) PDB : 2EFX; Ligand: NFA; Similar sites found: 11
This union binding pocket(no: 2) in the query (biounit: 2efx.bio6) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5DMM HCS 0.0133 0.40865 2.25806
2 1W7F ICT 0.01073 0.40873 2.28013
3 5UI2 SUC 0.00886 0.4089 2.83912
4 4PTN PYR 0.01984 0.40875 2.91545
5 4DNJ ANN 0.01197 0.40337 3.30579
6 3ICR FAD 0.04667 0.40018 3.30579
7 5NE2 DGL 0.0345 0.40157 3.95683
8 4DO1 ANN 0.01532 0.40075 4.40771
9 1Z6K OAA 0.008597 0.41224 6.14334
10 4WOH 4NP 0.01611 0.40328 7.22892
11 4JUI EGR 0.01764 0.40004 7.43802
Pocket No.: 3; Query (leader) PDB : 2EFX; Ligand: NFA; Similar sites found: 30
This union binding pocket(no: 3) in the query (biounit: 2efx.bio2) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4RJD TFP 0.01115 0.41026 None
2 4K91 SIN 0.00008881 0.51886 1.7341
3 4JF5 FLC 0.005289 0.4122 2.05761
4 5EOO CIT 0.001599 0.45402 2.26415
5 2Y91 98J 0.01198 0.41437 2.64151
6 5TG5 JW8 0.007518 0.42167 2.85714
7 2FN1 SAL 0.002252 0.43925 3.58127
8 5JXZ ISC 0.01109 0.40174 3.85675
9 5JXZ ISJ 0.01155 0.40092 3.85675
10 2WGV CIT 0.003248 0.44239 4.03226
11 2ZD8 MER 0.001508 0.41247 4.15094
12 5UJ3 CE4 0.0007778 0.42529 4.48276
13 3G2Y GF4 0.0003572 0.49686 4.56274
14 4DE0 0JB 0.0007193 0.46315 4.56274
15 4DDS 0J7 0.0005987 0.4611 4.56274
16 4DE2 DN3 0.001112 0.45402 4.56274
17 4UAA 3GK 0.0009047 0.45268 4.56274
18 4UA7 3GK 0.001011 0.45041 4.56274
19 4DDY DN6 0.001103 0.44864 4.56274
20 4DE1 0J6 0.0009568 0.44624 4.56274
21 4DE3 DN8 0.00167 0.43515 4.56274
22 1TDF NAP 0.03204 0.42638 4.74684
23 1TDF FAD 0.01776 0.42638 4.74684
24 3R75 BEZ 0.005546 0.42535 4.95868
25 3HUN ZZ7 0.01854 0.40241 6.33609
26 4KQR VPP 0.000516 0.42342 8.26446
27 3IHB GLU 0.0001029 0.52749 10.1928
28 1I7Q BEZ 0.0118 0.40447 14.5078
29 4P87 4NP 0.0006007 0.47323 19.8347
30 1YQS BSA 0.000002829 0.41527 44.4126
Pocket No.: 4; Query (leader) PDB : 2EFX; Ligand: NFA; Similar sites found: 3
This union binding pocket(no: 4) in the query (biounit: 2efx.bio5) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4L80 OXL 0.008125 0.4107 2.87356
2 4HP0 NOJ NAG NAG NAG 0.0363 0.40253 3.87597
3 2FAV APR 0.0206 0.41425 6.11111
Pocket No.: 5; Query (leader) PDB : 2EFX; Ligand: NFA; Similar sites found: 5
This union binding pocket(no: 5) in the query (biounit: 2efx.bio3) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5AWQ GLC GLC 0.01785 0.40714 1.92837
2 4M5P MLA 0.01299 0.40838 6.88705
3 1GXS BEZ 0.005831 0.42913 11.3924
4 3VPB GLU 0.01565 0.4093 23.2143
5 3HLF SIM 0.001759 0.40841 32.2314
Pocket No.: 6; Query (leader) PDB : 2EFX; Ligand: NFA; Similar sites found: 2
This union binding pocket(no: 6) in the query (biounit: 2efx.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4QIJ 1HA 0.04711 0.42065 2.69461
2 2V5E SCR 0.02565 0.40292 4
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