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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 253 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 209 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 173 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 PHE 0.657143 0.666667
3 DPN 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 with APoc: 66
This union binding pocket(no: 1) in the query (biounit: 2efx.bio4) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 6MPT C30 1.3986
2 4UP3 FAD 1.59236
3 4M52 FAD 1.71674
4 3EEL 53T 1.76211
5 2VGK REZ 1.92837
6 5HGZ ACO 2.05761
7 2H6T IVA VAL VAL STA ALA STA 2.35294
8 5WPJ NDP 2.47934
9 3C3N FMN 2.5641
10 2NVK FAD 2.75482
11 4CNK FAD 2.75482
12 2HQM FAD 2.75482
13 4EIL NDP 3.0303
14 3FQ8 PMP 3.30579
15 3ZYR ASN NAG NAG BMA MAN MAN NAG NAG 3.44828
16 3ZYR NAG NAG BMA MAN MAN NAG NAG 3.44828
17 2AR6 NAG MAN MAN MAN NAG 3.57143
18 2AR6 NAG MAN 3.57143
19 2AUY NAG MAN MMA 3.57143
20 3ZOK NAD 3.58127
21 1NVM NAD 3.84615
22 5ZW3 SAH 4
23 3HBF MYC 4.13223
24 1VDC FAD 4.2042
25 4X7G NAP 4.38247
26 3ITJ FAD 4.43787
27 5UJ3 CE4 4.48276
28 5FUS DAO 4.52962
29 6BT6 3GK 4.56274
30 4DDS 0J7 4.56274
31 4DE0 0JB 4.56274
32 4UAA 3GK 4.56274
33 4UA7 3GK 4.56274
34 4DE1 0J6 4.56274
35 4DDY DN6 4.56274
36 4DE2 DN3 4.56274
37 4DE3 DN8 4.56274
38 3NRR D16 4.6832
39 3NRR NAP 4.6832
40 3OIX FMN 4.92754
41 1GPE FAD 4.95868
42 1ZK7 FAD 5.23416
43 5J60 FAD 5.9375
44 3B1Q NOS 6.44172
45 6EDK 1YA 6.45161
46 4KM2 TOP 6.70391
47 4KM2 ATR 6.70391
48 1W8S FBP 6.84411
49 2Q7V FAD 7.38462
50 2CIG 1DG 7.54717
51 1U72 NDP 8.06452
52 1U72 MTX 8.06452
53 4KQR VPP 8.26446
54 3LL5 IPE 8.43373
55 4OR7 NAP 8.48485
56 2R2N KYN 10.1928
57 2R2N PMP 10.1928
58 1YLH PYR 10.4683
59 4OLT GCS GCS GCS GCS GCS GCS 12.5
60 2W9S NDP 14.2857
61 3RG9 NDP 16.6667
62 3RG9 WRA 16.6667
63 1PI5 SM2 25.1397
64 5ZA2 NXL 25.9887
65 1XS1 DUT 29.0155
66 1YQS BSA 44.4126
Pocket No.: 2; Query (leader) PDB : 2EFX; Ligand: NFA; Similar sites found with APoc: 51
This union binding pocket(no: 2) in the query (biounit: 2efx.bio6) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5O0J 8BR 1.65289
2 1JS3 PLP 142 1.65289
3 2Q0L FAD 1.92926
4 5F1R 42O 2.1097
5 1U70 NDP 2.15054
6 1U70 MTX 2.15054
7 5DMM HCS 2.25806
8 1W7F ICT 2.28013
9 4EU7 CIT 2.33463
10 2Z6J FMN 2.40964
11 2Z6I FMN 2.40964
12 4P5Z Q7M 2.49307
13 4QIJ 1HA 2.69461
14 3LZW NAP 2.71084
15 4DP3 NDP 2.75482
16 4DP3 MMV 2.75482
17 5UI2 SUC 2.83912
18 4PTN PYR 2.91545
19 1SG4 CO8 3.07692
20 5UQW GDP 3.1746
21 1J3I NDP 3.21429
22 3ICS FAD 3.30579
23 3ICR FAD 3.30579
24 4DNJ ANN 3.30579
25 3KJS DQ1 3.58127
26 6CGN DA 3.58127
27 4I4Z 2NE 3.63636
28 5ZYN FAD 3.85675
29 5TZJ UD1 4.13223
30 4DO1 ANN 4.40771
31 6AMI TRP 4.6832
32 1PZO CBT 4.94297
33 3NTA FAD 4.95868
34 3NTD FAD 4.95868
35 2HKA C3S 5.38462
36 3WGT FAD 5.76369
37 1YVD GNP 5.91716
38 2TPI ILE VAL 6.11354
39 1Z6K OAA 6.14334
40 1JBU BEN 6.34921
41 4WOH 4NP 7.22892
42 4JUI EGR 7.43802
43 5HCY 60D 8.76133
44 1AOE NDP 9.89583
45 1AOE GW3 9.89583
46 2O4C NAD 10.5263
47 1DR1 NAP 11.1111
48 1DR1 HBI 11.1111
49 5JBE GLC GLC GLC GLC GLC 12.6722
50 4LHW GNP 13.7931
51 5T9F TYR 14.7601
Pocket No.: 3; Query (leader) PDB : 2EFX; Ligand: NFA; Similar sites found with APoc: 55
This union binding pocket(no: 3) in the query (biounit: 2efx.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4RJD TFP None
2 1V2F HCI 1.37741
3 4K91 SIN 1.7341
4 1GET NAP 1.92837
5 4V3C C 1.92837
6 4JDR FAD 1.92837
7 4JF5 FLC 2.05761
8 2O1V ADP 2.20386
9 1OVD FMN 2.2508
10 1OVD ORO 2.2508
11 5EOO CIT 2.26415
12 5H4S RAM 2.46479
13 2Y91 98J 2.64151
14 5TG5 JW8 2.85714
15 1SJD NPG 3.30579
16 3NVD OAN 3.30579
17 2FN1 SAL 3.58127
18 5JXZ ISC 3.85675
19 5JXZ ISJ 3.85675
20 5YW5 ADE 3.91061
21 5NE2 DGL 3.95683
22 2WGV CIT 4.03226
23 3VEH 0GA 4.13223
24 2ZD8 MER 4.15094
25 3NY4 SMX 4.15094
26 4RJK TPP 4.40771
27 4ZCC FAD 4.46429
28 2VYN NAD 4.49102
29 3G2Y GF4 4.56274
30 2YPO PHE 4.6832
31 1K3T BRZ 4.73538
32 1TDF FAD 4.74684
33 1TDF NAP 4.74684
34 3R75 BEZ 4.95868
35 4LS7 1X9 5.50964
36 3HUN ZZ7 6.33609
37 6BU3 3GK 6.48855
38 3RYC GTP 6.99301
39 1N62 MCN 7.7135
40 1T3Q MCN 7.7381
41 1NZY BCA 8.55019
42 1JXZ BCA 8.55019
43 3IHB GLU 10.1928
44 4LNU GTP 10.6509
45 5EYP GDP 10.6509
46 5EIB GTP 10.6509
47 4LNU GDP 10.6509
48 5EYP GTP 10.6509
49 1WS1 BB2 10.8974
50 5ITZ GDP 14.1732
51 1I7Q BEZ 14.5078
52 5EYK 5U5 18.6441
53 4P87 4NP 19.8347
54 3VPB GLU 23.2143
55 3HLF SIM 32.2314
Pocket No.: 4; Query (leader) PDB : 2EFX; Ligand: NFA; Similar sites found with APoc: 22
This union binding pocket(no: 4) in the query (biounit: 2efx.bio5) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 3FHR P4O 1.19048
2 2PT9 2MH 1.86916
3 4GLJ RHB 2.0202
4 2I7C AAT 2.12014
5 3PFD FDA 2.20386
6 4WB7 ATP 2.20386
7 1SR7 MOF 2.3166
8 3ZLR X0B 2.53165
9 4E1Z 0MX 2.74914
10 4L80 OXL 2.87356
11 1PJS NAD 3.30579
12 5LAU AR6 4.32692
13 1FL2 FAD 4.51613
14 4DPL NAP 5.01393
15 5AB7 MLC 5.23416
16 1LUA NAP 5.57491
17 2FAV APR 6.11111
18 1USF NAP 6.17978
19 1USF FMN 6.17978
20 1EJ0 SAM 7.22222
21 3LL5 ADP 8.43373
22 3IX9 NDP 8.94737
Pocket No.: 5; Query (leader) PDB : 2EFX; Ligand: NFA; Similar sites found with APoc: 28
This union binding pocket(no: 5) in the query (biounit: 2efx.bio3) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 4RPL 3UC 1.65289
2 4RPL FAD 1.65289
3 1GET FAD 1.92837
4 5AWQ GLC GLC 1.92837
5 1V0C KNC 1.9802
6 1V0C ACO 1.9802
7 1QH9 LAC 2.15517
8 1PL6 572 2.24719
9 2CUN 3PG 2.75482
10 1ZPD DPX 3.0303
11 2E7Z MGD 3.30579
12 5WS9 AMP 3.58127
13 4YKG NAD 3.85675
14 4YKG FAD 3.85675
15 2RAB NAD 3.85675
16 2RAB FAD 3.85675
17 4TQK NAG 4.13223
18 6EK3 OUL 4.97738
19 1BZL FAD 5.23416
20 4YSX FAD 6.41026
21 3CQ5 PMP 6.88705
22 3RYC GDP 6.99301
23 2F5Z FAD 7.98898
24 4EWH T77 8
25 3FUR Z12 10.2941
26 1GXS BEZ 11.3924
27 5ODQ FAD 13.5714
28 4LHD GLY 15.7025
Pocket No.: 6; Query (leader) PDB : 2EFX; Ligand: NFA; Similar sites found with APoc: 21
This union binding pocket(no: 6) in the query (biounit: 2efx.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1CER NAD 2.1148
2 3F8D FAD 2.16718
3 1GAD NAD 2.42424
4 3CMC NAD 2.69461
5 2B9W FAD 2.75482
6 1GTE FAD 3.30579
7 2ITM XUL 3.30579
8 2V5E SCR 4
9 3L4S 3PG 4.16667
10 3L4S NAD 4.16667
11 4ZCC NAI 4.46429
12 5LP1 71H 4.95868
13 4J56 FAD 5.26316
14 1N46 PFA 5.81395
15 3NWQ 2NC 6.06061
16 2B4R AES 6.66667
17 5LXT GDP 6.99301
18 5LXT 7AK 6.99301
19 4ONC 40B 7.04225
20 5JY6 NAD 8.70786
21 5EYP LOC 10.6509
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