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Receptor
PDB id Resolution Class Description Source Keywords
4BA5 1.76 Å EC: 2.6.1.18 CRYSTAL STRUCTURE OF OMEGA-TRANSAMINASE FROM CHROMOBACTERIUM VIOLACEUM CHROMOBACTERIUM VIOLACEUM TRANSFERASE
Ref.: STRUCTURAL STUDIES WITH PSEUDOMONAS AND CHROMOBACTE [OMEGA]-AMINOTRANSFERASES PROVIDE INSIGHTS INTO THE DIFFERING SUBSTRATE SPECIFICITY. ACTA CRYSTALLOGR.,SECT.D V. 69 564 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 B:1460;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
PXG B:470;
A:470;
Valid;
Valid;
none;
none;
submit data
368.278 C15 H17 N2 O7 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4BA5 1.76 Å EC: 2.6.1.18 CRYSTAL STRUCTURE OF OMEGA-TRANSAMINASE FROM CHROMOBACTERIUM VIOLACEUM CHROMOBACTERIUM VIOLACEUM TRANSFERASE
Ref.: STRUCTURAL STUDIES WITH PSEUDOMONAS AND CHROMOBACTE [OMEGA]-AMINOTRANSFERASES PROVIDE INSIGHTS INTO THE DIFFERING SUBSTRATE SPECIFICITY. ACTA CRYSTALLOGR.,SECT.D V. 69 564 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4BA5 - PXG C15 H17 N2 O7 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 3 families.
1 4BA5 - PXG C15 H17 N2 O7 P Cc1c(c(c(c....
50% Homology Family (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6FYQ - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 4WYC Kd = 15 uM 3VS C10 H9 N3 O c1cc(ccc1C....
3 4CXR - 2BG C8 H8 N2 S c1ccc2c(c1....
4 3TFU - PL8 C16 H22 N3 O7 P Cc1c(c(c(c....
5 4MQR - 2B9 C14 H15 N4 O6 P CC1=C(/C(=....
6 4MQP - 2B1 C15 H15 N4 O5 P S Cc1c(c(c(c....
7 4XJO Kd = 132 nM 41O C20 H17 Cl N2 O2 c1cc(cc(c1....
8 5KGS Kd = 74 nM 6SR C21 H20 N2 O4 c1cc2c(cc1....
9 4W1W ic50 = 0.195 uM 3G8 C18 H17 N O3 S CCN(CC)c1c....
10 4WYG Kd = 6.8 uM 3W1 C11 H12 Cl N3 c1cc(ccc1C....
11 4MQQ - 2B6 C16 H15 N4 O6 P S Cc1c(c(c(c....
12 4XEW ic50 = 0.44 uM 40N C16 H10 F N O3 c1ccc(c(c1....
13 4W1V ic50 = 0.659 uM 3GS C16 H14 F N O5 S COC(=O)c1c....
14 4XJP Kd = 108 nM 41N C20 H20 N2 O4 CC(=O)c1cc....
15 4WYF Kd = 21.7 uM 3VX C11 H9 N O2 CC(=O)Nc1c....
16 4WYA Kd = 6.9 uM 3VQ C10 H8 N2 O S c1ccnc(c1)....
17 4W1X - 3G9 C19 H19 Cl N2 O2 CC(=O)c1cc....
18 5KGT - 6SQ C20 H20 Cl N O2 CC(=O)c1cc....
19 4WYE Kd = 41.8 uM 3VW C12 H15 N O c1ccc(cc1)....
20 4CXQ - KAP C9 H17 N O3 C[C@@H](C(....
21 4WYD Kd = 11.7 uM 3VR C12 H15 N3 CNCc1ccc(c....
22 3LV2 - SFG C15 H23 N7 O5 c1nc(c2c(n....
23 5TE2 - 7B9 C16 H22 N3 O7 P Cc1c(c(c(c....
24 4B9B - PLP C8 H10 N O6 P Cc1c(c(c(c....
25 4B98 - PXG C15 H17 N2 O7 P Cc1c(c(c(c....
26 1MLZ - TZA PLP n/a n/a
27 1MLY - ACZ PLP n/a n/a
28 1S07 - PLP C8 H10 N O6 P Cc1c(c(c(c....
29 3DU4 - KAP C9 H17 N O3 C[C@@H](C(....
30 4BA5 - PXG C15 H17 N2 O7 P Cc1c(c(c(c....
31 3A8U - PLP C8 H10 N O6 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PXG; Similar ligands found: 56
No: Ligand ECFP6 Tc MDL keys Tc
1 PXG 1 1
2 GBC PLP 0.670732 0.95
3 GAB PLP 0.670732 0.95
4 PSZ 0.641975 0.892308
5 PLG 0.551282 0.873016
6 PLA 0.542169 0.820895
7 PDA 0.530864 0.887097
8 PP3 0.530864 0.887097
9 PDD 0.530864 0.887097
10 P1T 0.530864 0.833333
11 C6P 0.53012 0.873016
12 RW2 0.52809 0.835821
13 IK2 0.52439 0.833333
14 5PA 0.518072 0.861538
15 PMH 0.518072 0.753425
16 PLS 0.518072 0.873016
17 2BO 0.518072 0.887097
18 2BK 0.518072 0.887097
19 TLP 0.518072 0.887097
20 PPD 0.511905 0.873016
21 7TS 0.511628 0.714286
22 CBA 0.511628 0.846154
23 PY5 0.505882 0.820895
24 QLP 0.505747 0.797101
25 PMG 0.505747 0.797101
26 PDG 0.494253 0.846154
27 ILP 0.494253 0.859375
28 7XF 0.494253 0.846154
29 PGU 0.494253 0.846154
30 IN5 0.493827 0.854839
31 LPI 0.488636 0.785714
32 PY6 0.483146 0.797101
33 HEY 0.483146 0.820895
34 76U 0.483146 0.833333
35 AQ3 0.479167 0.936508
36 N5F 0.477778 0.833333
37 EA5 0.477778 0.808824
38 ORX 0.477778 0.833333
39 3LM 0.477778 0.797101
40 PL8 0.473118 0.767123
41 PE1 0.472527 0.833333
42 33P 0.470588 0.84127
43 PXP 0.466667 0.8
44 PL4 0.462366 0.833333
45 PMP 0.460526 0.866667
46 DCS 0.455556 0.723684
47 PL2 0.455556 0.742857
48 GT1 0.454545 0.71875
49 KAM 0.452632 0.833333
50 7B9 0.447917 0.8
51 1D0 0.434343 0.921875
52 0LD 0.433962 0.707317
53 ACZ PLP 0.43 0.890625
54 TZA PLP 0.43 0.890625
55 9YM 0.425532 0.818182
56 PLR 0.413333 0.704918
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4BA5; Ligand: PXG; Similar sites found with APoc: 126
This union binding pocket(no: 1) in the query (biounit: 4ba5.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 6EGU 43Y 1.08932
2 1PMO PLR 1.30719
3 2X5F PLP 1.39535
4 2Z9V PXM 1.78571
5 3B8X G4M 1.79487
6 5W71 9YM 1.81818
7 5W71 PLP 1.81818
8 1DJ9 KAM 1.82292
9 1M32 PLP 1.91257
10 2TPL HPP 1.97368
11 6ECG PM9 1.97802
12 4IY7 KOU 2.01511
13 4IY7 0JO 2.01511
14 4IYO 0JO 2.01511
15 1NAA ABL 2.17865
16 1NAA 6FA 2.17865
17 4Q4K FMN 2.2409
18 2FNU PMP UD1 2.4
19 1EI6 PPF 2.46305
20 3PD6 PMP 2.49377
21 3PDB PMP 2.49377
22 3NUB UD0 2.50696
23 1TZD ADP 2.54545
24 3WGC PLG 2.6393
25 2D09 FLV 2.7027
26 2PO3 T4K 2.83224
27 1M7Y PPG 2.83224
28 1B9I PXG 2.83505
29 2HHP FLC 3.05011
30 2C1X UDP 3.05011
31 1OXO IK2 3.2419
32 1FC4 AKB PLP 3.26797
33 6CD1 PLS 3.2967
34 6CD1 PLG 3.2967
35 3DR4 G4M 3.32481
36 2P3V SRT 3.51562
37 4RKC PMP 3.51759
38 1CL2 PPG 3.5443
39 5W19 9TD 3.7037
40 4ZUL UN1 3.7037
41 1LW4 PLP 3.7464
42 1LW4 TLP 3.7464
43 4ZAH T5K 3.78788
44 1ELU CSS 3.84615
45 1ELU PDA 3.84615
46 1GCK ASP PLP 3.8961
47 1E5F PLP 3.9604
48 2P4Y C03 3.97112
49 2FYF PLP 4.0201
50 2WK9 PLG 4.11311
51 2WK9 PLP 4.11311
52 5VEQ PMP 4.13625
53 4AZJ SEP PLP 4.13943
54 6BKA FMN 4.13943
55 4K2M O1G 4.28894
56 6GNF GLC 4.3573
57 3ZRR PXG 4.57516
58 2R5C C6P 4.662
59 2R5E QLP 4.662
60 6EWR PMP 4.68384
61 4UP3 FAD 4.77707
62 5U23 TQP 4.79303
63 4LNL PLG 4.8048
64 4LNL 2BO 4.8048
65 4LNL 2BK 4.8048
66 1AJS PLA 4.85437
67 6DND PLP 4.86618
68 5K8B PDG 4.96278
69 1DFO PLG 5.03597
70 4M2K PLP 5.17241
71 5X2Z 3LM 5.27638
72 5X30 4LM 5.27638
73 5X30 7XF 5.27638
74 1O69 X04 5.32995
75 2XBN PMP 5.38642
76 5W70 9YM 5.39326
77 1SJD NPG 5.43478
78 3THR C2F 5.46075
79 1K1Y MAL 5.66449
80 2VAR KDG 5.7508
81 2VAR KDF 5.7508
82 3VP6 HLD 6.10022
83 5M3Z PLP 6.28141
84 5M3Z PY6 6.28141
85 5M3Z NLE 6.28141
86 2HW1 FRU 6.37584
87 2ZC0 PMP 6.38821
88 1VJO PLP 6.61578
89 1U08 PLP 6.73575
90 6C8T EQJ 6.91489
91 6C92 EQJ 6.91489
92 2OGA PGU 7.01754
93 1MDZ DCS 7.12468
94 1MDZ PLP 7.12468
95 3FRK TQP 7.5067
96 1K4M CIT 7.51174
97 5YKT PMP 7.84314
98 5TXR PLP 7.84314
99 5GVL GI8 7.91855
100 5GVL PLG 7.91855
101 1U26 IHS 8.01187
102 1T0S BML 8.13953
103 4HVK PMP 8.37696
104 1WYV PLP AOA 10.6754
105 4WXG 2BO 12.4183
106 1LC8 33P 14.011
107 5DDW 5B6 17.4292
108 2CJH AKG 22.7171
109 6CBN OZY 24.4292
110 6CBO DOW 24.6014
111 4AOA IK2 25.7081
112 4ZSY RW2 25.7081
113 3BS8 PMP 28.7671
114 3FQ8 PMP 33.0211
115 4ZM4 PLP 37.3602
116 4ZM4 P3B 37.3602
117 4UOX PLP 39.6514
118 4UOX PUT 39.6514
119 4UOX PLP PUT 39.6514
120 5G09 6DF 43.1373
121 2OAT PFM 43.2802
122 1SFF IK2 43.662
123 5G4J EXT 44.1704
124 5WYF ILP 44.8802
125 4ADC PLP 47.0443
126 1ZC9 PMP 47.3441
Pocket No.: 2; Query (leader) PDB : 4BA5; Ligand: PXG; Similar sites found with APoc: 30
This union binding pocket(no: 2) in the query (biounit: 4ba5.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1JS3 PLP 142 1.96078
2 4M52 FAD 2.17865
3 1TOI HCI 2.52525
4 3RHJ NAP 2.61438
5 3BW2 FMN 2.71003
6 2HOX P1T 2.83224
7 3B1Q NOS 2.83224
8 4XDA RIB 2.91262
9 2JBM SRT 3.01003
10 4LZJ 22H 3.30033
11 3KYF 5GP 5GP 3.4632
12 4AT0 FAD 3.48584
13 4D9M 0JO 3.51759
14 2IOR ADP 3.82979
15 3HQ9 OXL 4.05797
16 5XH2 NPO 4.19847
17 4C3Y ANB 4.79303
18 2A2C NG1 5.43933
19 2A2C ADP 5.43933
20 2ZYJ PGU 5.44662
21 4E1O PLP PVH 6.65281
22 5XM3 PQQ 6.66667
23 6C9B EGV 6.91489
24 1H74 ADP 7.09459
25 4RT1 C2E 8.03571
26 1GEX PLP HSA 8.27887
27 2D0V PQQ 8.33333
28 2F5Z FAD 9.375
29 4YGF AZM 18.3761
30 3RNM FAD 18.9655
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