Receptor
PDB id Resolution Class Description Source Keywords
4RKC 2.19 Å EC: 2.6.1.57 PSYCHROPHILIC AROMATIC AMINO ACIDS AMINOTRANSFERASE FROM PSY SP. B6 PSYCHROBACTER SP. B6 AMINOTRANSFERASE AROMATIC SUBSTRATES PLP DEPENDENT ENZYMETRANSFERASE
Ref.: CRYSTAL STRUCTURE AND ENZYMATIC PROPERTIES OF A BRO SUBSTRATE-SPECIFICITY PSYCHROPHILIC AMINOTRANSFERAS THE ANTARCTIC SOIL BACTERIUM, PSYCHROBACTER SP. B6 ACTA CRYSTALLOGR.,SECT.D V. 71 632 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:401;
B:401;
Invalid;
Invalid;
none;
none;
submit data
24.305 Mg [Mg+2...
PMP A:409;
B:405;
Valid;
Valid;
none;
none;
submit data
248.173 C8 H13 N2 O5 P Cc1c(...
NO3 A:405;
A:404;
A:408;
B:404;
B:402;
A:403;
A:402;
B:403;
A:406;
A:407;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.005 N O3 [N+](...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4RKC 2.19 Å EC: 2.6.1.57 PSYCHROPHILIC AROMATIC AMINO ACIDS AMINOTRANSFERASE FROM PSY SP. B6 PSYCHROBACTER SP. B6 AMINOTRANSFERASE AROMATIC SUBSTRATES PLP DEPENDENT ENZYMETRANSFERASE
Ref.: CRYSTAL STRUCTURE AND ENZYMATIC PROPERTIES OF A BRO SUBSTRATE-SPECIFICITY PSYCHROPHILIC AMINOTRANSFERAS THE ANTARCTIC SOIL BACTERIUM, PSYCHROBACTER SP. B6 ACTA CRYSTALLOGR.,SECT.D V. 71 632 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4RKC - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4RKC - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
50% Homology Family (71)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2AY8 Kd = 5.8 mM 4TB C8 H10 O2 S c1cc(sc1)C....
2 2AY4 Kd = 1.24 mM PPT C10 H12 O2 Cc1ccc(cc1....
3 2AY7 Kd = 5 mM CLT C10 H12 O2 c1ccc(cc1)....
4 2AY3 Kd = 0.28 mM MPP C11 H14 O4 COc1ccc(cc....
5 1AY8 - HCI C9 H10 O2 c1ccc(cc1)....
6 1AY5 - MAE C4 H4 O4 C(=C/C(=O)....
7 2AY9 Kd = 6.9 mM 5PV C11 H14 O2 c1ccc(cc1)....
8 2AY6 Kd = 0.78 mM 3IB C12 H13 N O2 c1ccc2c(c1....
9 2AY2 Kd = 13.1 mM CXP C9 H16 O2 C1CCC(CC1)....
10 2AY5 Kd = 2.6 mM IOP C11 H11 N O2 c1ccc2c(c1....
11 2AY1 Kd = 5.14 mM AHC C9 H11 N O2 c1cc(ccc1C....
12 1X2A - PDG C13 H19 N2 O9 P Cc1c(c(c(c....
13 1CZE Kd = 2.4 mM SIN C4 H6 O4 O=C([O-])C....
14 1AHX Kd = 120 uM HCI C9 H10 O2 c1ccc(cc1)....
15 3PAA - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
16 3QPG - 3QP C13 H16 N O9 P Cc1ccc(c(c....
17 1QIT - MAE C4 H4 O4 C(=C/C(=O)....
18 2QBT - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
19 1TOI Kd = 0.09 mM HCI C9 H10 O2 c1ccc(cc1)....
20 1ASC - NPL C9 H16 N2 O5 P Cc1c(c(c(c....
21 1ASA - MAE C4 H4 O4 C(=C/C(=O)....
22 1ARH - PPD C12 H17 N2 O9 P Cc1c(c(c(c....
23 1CZC Kd = 1.5 mM GUA C5 H8 O4 C(CC(=O)O)....
24 1X29 - PMG C14 H21 N2 O9 P Cc1c(c(c(c....
25 1QIS - MAE C4 H4 O4 C(=C/C(=O)....
26 1AMQ - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
27 4A00 - PP3 C11 H17 N2 O7 P Cc1c(c(c(c....
28 1IX7 - MAE C4 H4 O4 C(=C/C(=O)....
29 1AMR - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
30 1TOK Kd = 3.4 mM MAE C4 H4 O4 C(=C/C(=O)....
31 1ASM - MAE C4 H4 O4 C(=C/C(=O)....
32 5VWQ - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
33 1AHG - PLP TYR n/a n/a
34 5VWR - PL6 C13 H17 N2 O9 P Cc1c(c(c(c....
35 1AHF - IOP C11 H11 N O2 c1ccc2c(c1....
36 2QB2 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
37 3ZZK - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
38 3PA9 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
39 1B4X - MAE C4 H4 O4 C(=C/C(=O)....
40 1X28 - PGU C13 H19 N2 O9 P Cc1c(c(c(c....
41 1YOO - IVA C5 H10 O2 CC(C)CC(=O....
42 1TOJ Kd = 0.41 mM HCI C9 H10 O2 c1ccc(cc1)....
43 1SPA - NPL C9 H16 N2 O5 P Cc1c(c(c(c....
44 2Q7W - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
45 1TOG Kd = 0.6 mM HCI C9 H10 O2 c1ccc(cc1)....
46 4DBC - 3QP C13 H16 N O9 P Cc1ccc(c(c....
47 1AIA - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
48 1ART - PLP 0A0 n/a n/a
49 1CQ7 - PY5 C13 H21 N2 O7 P CCC[C@@H](....
50 1ASD - MAE C4 H4 O4 C(=C/C(=O)....
51 1C9C - PP3 C11 H17 N2 O7 P Cc1c(c(c(c....
52 1CQ8 - PY6 C14 H23 N2 O7 P CCCC[C@@H]....
53 2QA3 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
54 1QIR - MAE C4 H4 O4 C(=C/C(=O)....
55 1ARG - PPD C12 H17 N2 O9 P Cc1c(c(c(c....
56 1AIC - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
57 1AHY Kd = 440 uM MAE C4 H4 O4 C(=C/C(=O)....
58 2QB3 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
59 1MAP - KET C12 H16 N2 O9 P Cc1c(c(c(c....
60 1AKC - PPE C13 H20 N2 O9 P Cc1c(c(c(c....
61 1AMA - PLA C13 H19 N2 O9 P Cc1c(c(c(c....
62 1AKB - PPD C12 H17 N2 O9 P Cc1c(c(c(c....
63 1IVR - CBA C12 H17 N2 O11 P Cc1c(c(c(c....
64 1AKA - PLP C8 H10 N O6 P Cc1c(c(c(c....
65 1MAQ - PGU C13 H19 N2 O9 P Cc1c(c(c(c....
66 9AAT - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
67 1OXP - IK2 C10 H15 N2 O8 P Cc1c(c(c(c....
68 1OXO - IK2 C10 H15 N2 O8 P Cc1c(c(c(c....
69 4RKC - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
70 2CST - MAE C4 H4 O4 C(=C/C(=O)....
71 1YAA - MAE C4 H4 O4 C(=C/C(=O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PMP; Similar ligands found: 78
No: Ligand ECFP6 Tc MDL keys Tc
1 PMP 1 1
2 PXP 0.7 0.888889
3 GT1 0.673077 0.793103
4 PLG 0.57377 0.866667
5 IN5 0.57377 0.912281
6 P1T 0.571429 0.825397
7 PLR 0.557692 0.781818
8 2BO 0.553846 0.881356
9 TLP 0.553846 0.881356
10 2BK 0.553846 0.881356
11 PP3 0.546875 0.881356
12 PDA 0.546875 0.881356
13 PDD 0.546875 0.881356
14 ILP 0.544118 0.852459
15 33P 0.538462 0.896552
16 IK2 0.538462 0.825397
17 5PA 0.530303 0.825397
18 PLS 0.530303 0.866667
19 PMH 0.530303 0.742857
20 PLP 0.527273 0.767857
21 C6P 0.522388 0.866667
22 PPD 0.522388 0.866667
23 ORX 0.521127 0.854839
24 PXM 0.52 0.735849
25 PZP 0.517857 0.836364
26 PLA 0.514706 0.8125
27 PY5 0.514706 0.8125
28 PL2 0.514286 0.84127
29 QLP 0.514286 0.815385
30 PE1 0.513889 0.854839
31 PPG 0.513514 0.825397
32 P0P 0.508772 0.8
33 HEY 0.507042 0.8125
34 CBA 0.5 0.83871
35 PGU 0.5 0.83871
36 7TS 0.5 0.702703
37 EA5 0.5 0.828125
38 3LM 0.5 0.787879
39 PDG 0.5 0.83871
40 7XF 0.5 0.83871
41 9YM 0.493151 0.868852
42 LCS 0.492958 0.675676
43 PMG 0.492958 0.787879
44 DCS 0.492958 0.712329
45 76U 0.486111 0.825397
46 PY6 0.486111 0.787879
47 PL4 0.48 0.854839
48 PSZ 0.479452 0.8
49 N5F 0.479452 0.825397
50 4LM 0.462687 0.725806
51 0JO 0.462687 0.714286
52 AN7 0.461538 0.741379
53 PXG 0.460526 0.866667
54 RW2 0.460526 0.8
55 FOO 0.454545 0.75
56 PL8 0.454545 0.732394
57 GLY PLP 0.454545 0.779661
58 NPL 0.45 0.898305
59 KAM 0.448718 0.825397
60 1D0 0.444444 0.8
61 7B9 0.443038 0.764706
62 2B1 0.443038 0.690141
63 P3D 0.442857 0.85
64 PLP SER 0.441176 0.779661
65 EPC 0.439394 0.789474
66 MP5 0.438596 0.728814
67 EXT 0.432836 0.79661
68 PLP PMP 0.432836 0.770492
69 AQ3 0.426829 0.8125
70 2B6 0.426829 0.662162
71 PLP ALO 0.422535 0.833333
72 MPM 0.414286 0.75
73 KOU 0.408451 0.8
74 SER PLP 0.402778 0.813559
75 HCP 0.402778 0.741935
76 PLP 2TL 0.402778 0.79661
77 Z98 0.4 0.777778
78 PFM 0.4 0.770492
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RKC; Ligand: PMP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4rkc.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4RKC; Ligand: PMP; Similar sites found: 80
This union binding pocket(no: 2) in the query (biounit: 4rkc.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2WK9 PLG 0.005078 0.43595 1.02828
2 2WK9 PLP 0.005317 0.43242 1.02828
3 5X2Z 3LM 0.001195 0.45752 1.25628
4 5X30 7XF 0.0004325 0.44011 1.25628
5 5X30 4LM 0.003931 0.40699 1.25628
6 2PO3 T4K 0.001719 0.46136 1.50754
7 3VP6 HLD 0.007449 0.41833 1.75879
8 4E3Q PMP 0.005344 0.40138 1.75879
9 1ELU PDA 0.0008015 0.4543 1.79487
10 1ELU CSS 0.002549 0.4351 1.79487
11 5U23 TQP 0.0005292 0.48219 1.83246
12 4AZJ SEP PLP 0.001064 0.45273 2.22222
13 1US5 GLU 0.008249 0.4056 2.2293
14 4QM9 CYS 0.01423 0.40779 2.31214
15 5MX4 HPA 0.007125 0.42484 2.57511
16 2HOX P1T 0.0000001055 0.63241 2.76382
17 3WGC PLG 0.0008135 0.44028 2.93255
18 5GVL PLG 0.006853 0.43734 3.01508
19 5GVL GI8 0.006853 0.43734 3.01508
20 1PMO PLR 0.001505 0.43101 3.01508
21 1LC8 33P 0.00691 0.45066 3.02198
22 3DR4 G4M 0.0005787 0.48948 3.06905
23 1LW4 PLP 0.002001 0.43172 3.17003
24 1LW4 TLP 0.002586 0.43093 3.17003
25 1DJ9 KAM 0.0006112 0.45508 3.38542
26 5W71 9YM 0.001089 0.47813 3.51759
27 5W71 PLP 0.0003284 0.46976 3.51759
28 4BA5 PXG 0.005786 0.41079 3.51759
29 4IY7 0JO 0.0006706 0.45999 3.52645
30 4IY7 KOU 0.0007285 0.45833 3.52645
31 4IYO 0JO 0.0005979 0.42658 3.52645
32 5JXZ ISC 0.01083 0.40041 3.58056
33 2FN1 PYR 0.0102 0.41451 3.76884
34 1FC4 AKB PLP 0.002058 0.40394 3.76884
35 1GEX PLP HSA 0.001919 0.47782 3.93258
36 2OGA PGU 0.001064 0.45272 4.0201
37 3E2Y PMP 0.00000004748 0.64732 4.27136
38 5EYP GTP 0.01977 0.401 4.27136
39 1WYV PLP AOA 0.001688 0.41965 4.52261
40 1JS3 PLP 142 0.002196 0.40855 4.52261
41 4JE5 PMP 0.0000001476 0.59483 4.77387
42 4JE5 PLP 0.0000001836 0.59098 4.77387
43 4E1O PLP PVH 0.005535 0.42117 4.77387
44 3NUB UD0 0.0002169 0.50091 5.01393
45 5W70 9YM 0.0003691 0.47197 5.02513
46 2FYF PLP 0.001099 0.42396 5.02513
47 5DJ3 5DK 0.0001546 0.48711 5.85106
48 4K2M O1G 0.0002517 0.42936 6.03015
49 1C7O PPG 0.0003497 0.47305 6.28141
50 4ZAH T5K 0.0001835 0.40523 6.81818
51 2R5C C6P 0.0000001141 0.634 7.03518
52 2R5E QLP 0.0000001128 0.5688 7.03518
53 3FQ8 PMP 0.009183 0.41248 7.28643
54 5D9O BGC BGC BGC BGC 0.01414 0.41866 7.36544
55 4M2K PLP 0.004308 0.43548 8.0402
56 5EOO CIT 0.01501 0.41323 8.67924
57 1XI9 PLP 0.000001262 0.54483 9.04523
58 5K8B PDG 0.000278 0.48184 9.29648
59 1DFO PLG 0.001652 0.44192 9.29648
60 3BWN PMP 0.0000007887 0.59104 9.46292
61 3BWN PMP PHE 0.000002041 0.51305 9.46292
62 3EI9 PL6 0.0000004728 0.51963 10.3015
63 1U08 PLP 0.0000001403 0.6354 10.3627
64 4FL0 PLP 0.0000009956 0.57078 10.5528
65 4R5Z PMP 0.000003223 0.49708 11.1717
66 4R5Z SIN 0.000007385 0.44961 11.1717
67 3B1E P1T 0.00003704 0.50739 11.2245
68 3CQ5 PMP 0.0000005246 0.62842 13.2791
69 5IWQ PLP 0.000001603 0.57683 13.5945
70 1GDE GLU PLP 0.000000936 0.54498 14.3959
71 2X5D PLP 0.0000002763 0.54744 15.8291
72 2ZYJ PGU 0.0000001112 0.50935 16.3728
73 2R2N PMP 0.000000003974 0.69699 17.5879
74 2R2N KYN 0.00000007565 0.48232 17.5879
75 1MDZ DCS 0.00505 0.43729 18.0662
76 1MDZ PLP 0.004766 0.43729 18.0662
77 1GCK ASP PLP 0.00000005942 0.64708 19.4805
78 2ZC0 PMP 0.0000000003417 0.74267 20.603
79 1UU1 PMP HSA 0.000000336 0.61523 23.2836
80 2X5F PLP 0.0000000002946 0.70702 29.397
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