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Receptor
PDB id Resolution Class Description Source Keywords
4ZM4 2.4 Å EC: 2.-.-.- COMPLEX STRUCTURE OF PCTV K276R MUTANT WITH PMP AND 3-DEHYDR STREPTOMYCES PACTUM PYRIDOXAL 5-PHOSPHATE AMINOTRANSFERASE TRANSFERASE
Ref.: MECHANISM-BASED TRAPPING OF THE QUINONOID INTERMEDI USING THE K276R MUTANT OF PLP-DEPENDENT 3-AMINOBENZ SYNTHASE PCTV IN THE BIOSYNTHESIS OF PACTAMYCIN. CHEMBIOCHEM V. 16 2484 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
P3B B:501;
E:501;
Valid;
Valid;
none;
none;
submit data
402.293 C15 H19 N2 O9 P CC1=C...
PLP C:501;
F:501;
A:501;
D:501;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4ZM4 2.4 Å EC: 2.-.-.- COMPLEX STRUCTURE OF PCTV K276R MUTANT WITH PMP AND 3-DEHYDR STREPTOMYCES PACTUM PYRIDOXAL 5-PHOSPHATE AMINOTRANSFERASE TRANSFERASE
Ref.: MECHANISM-BASED TRAPPING OF THE QUINONOID INTERMEDI USING THE K276R MUTANT OF PLP-DEPENDENT 3-AMINOBENZ SYNTHASE PCTV IN THE BIOSYNTHESIS OF PACTAMYCIN. CHEMBIOCHEM V. 16 2484 2015
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 269 families.
1 4ZM3 - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 4ZM4 - PLP C8 H10 N O6 P Cc1c(c(c(c....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 237 families.
1 4ZM3 - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 4ZM4 - PLP C8 H10 N O6 P Cc1c(c(c(c....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 187 families.
1 4ZM3 - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 4ZM4 - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 3FQA - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: P3B; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 P3B 1 1
2 PLI 0.530864 0.877193
3 PM9 0.472527 0.769231
4 P71 0.457447 0.87931
5 2B9 0.457447 0.765625
6 EMS 0.443299 0.806452
7 EJ1 0.438776 0.784615
8 P61 0.425743 0.8125
Ligand no: 2; Ligand: PLP; Similar ligands found: 62
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP 1 1
2 PZP 0.729167 0.843137
3 EXT 0.62069 0.8
4 AN7 0.603448 0.918367
5 EPC 0.603448 0.862745
6 FOO 0.59322 0.849057
7 PLR 0.58 0.895833
8 4LM 0.57377 0.818182
9 0JO 0.57377 0.803571
10 P3D 0.571429 0.704918
11 F0G 0.564516 0.865385
12 MPM 0.564516 0.814815
13 FEV 0.555556 0.803571
14 KOU 0.555556 0.836364
15 HCP 0.546875 0.77193
16 EVM 0.546875 0.821429
17 6DF 0.545455 0.811321
18 PXL 0.541667 0.659574
19 Z98 0.537313 0.75
20 PXP 0.537037 0.862745
21 PMP 0.527273 0.767857
22 P0P 0.527273 0.916667
23 PL6 0.522388 0.818182
24 GT1 0.517857 0.830189
25 PFM 0.514706 0.803571
26 FEJ 0.514706 0.851852
27 LLP 0.5 0.737705
28 P70 0.5 0.833333
29 PUS 0.479452 0.707692
30 PL5 0.479452 0.775862
31 MPL 0.473684 0.836364
32 PLG 0.46875 0.75
33 IN5 0.46875 0.758621
34 P89 0.466667 0.714286
35 PLP PUT 0.463768 0.672131
36 EQJ 0.460526 0.725806
37 5DK 0.460526 0.725806
38 O1G 0.454545 0.75
39 PLT 0.439024 0.762712
40 X04 0.431034 0.851852
41 PDD 0.426471 0.762712
42 PP3 0.426471 0.762712
43 PDA 0.426471 0.762712
44 P1T 0.426471 0.714286
45 33P 0.42029 0.745763
46 IK2 0.42029 0.714286
47 TLP 0.414286 0.793103
48 2BK 0.414286 0.793103
49 PLS 0.414286 0.779661
50 2BO 0.414286 0.793103
51 5PA 0.414286 0.714286
52 PMH 0.414286 0.619718
53 9TD 0.413793 0.671642
54 PLP 999 0.410959 0.796296
55 PPD 0.408451 0.75
56 C6P 0.408451 0.75
57 QLP 0.405405 0.681818
58 MP5 0.403509 0.666667
59 PLA 0.402778 0.703125
60 PY5 0.402778 0.703125
61 HEY 0.4 0.703125
62 PLP PHE 0.4 0.732143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4ZM4; Ligand: PLP; Similar sites found with APoc: 144
This union binding pocket(no: 1) in the query (biounit: 4zm4.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 6EWR PMP 1.40515
2 1E5F PLP 1.48515
3 5M3Z PY6 1.50754
4 5M3Z NLE 1.50754
5 5M3Z PLP 1.50754
6 4IY7 KOU 1.76322
7 4IY7 0JO 1.76322
8 4IYO 0JO 1.76322
9 5W19 9TD 1.78971
10 3X0D SAH 1.78971
11 2Q7V FAD 1.84615
12 5JGA 6KC 1.90476
13 6CZY PMP 1.9337
14 4Z24 FAD 2.01342
15 4JDR FAD 2.01342
16 1LW4 TLP 2.01729
17 1LW4 PLP 2.01729
18 3DR4 G4M 2.04604
19 3B8X G4M 2.05128
20 2R5C C6P 2.0979
21 2R5E QLP 2.0979
22 6C3C EJ1 2.17918
23 5K8B PDG 2.23325
24 4HA6 FAD 2.23714
25 5X2Z 3LM 2.26131
26 5X30 4LM 2.26131
27 5X30 7XF 2.26131
28 4ZAH T5K 2.27273
29 1S16 ANP 2.30769
30 4HVK PMP 2.35602
31 1DFO PLG 2.39808
32 1AJS PLA 2.42718
33 2ZC0 PMP 2.457
34 1PMO PLR 2.46085
35 2UYT LRH 2.46085
36 2UYT ADP 2.46085
37 2FYF PLP 2.51256
38 5BSR AMP 2.68456
39 5X40 ACP 2.73973
40 2HIM ASN 2.7933
41 1VJO PLP 2.79898
42 1B9I PXG 2.83505
43 1GCK ASP PLP 2.85714
44 1JS3 PLP 142 2.90828
45 5ERG SAM 2.90828
46 6C9B EGV 2.92553
47 5W71 9YM 2.95455
48 5W71 PLP 2.95455
49 4E1O PLP PVH 3.13199
50 6ECG PM9 3.13199
51 2TPL HPP 3.13199
52 4K2M O1G 3.16027
53 3FRK TQP 3.21716
54 2Z9V PXM 3.31633
55 5ECP ATP 3.3557
56 5ECP MET 3.3557
57 5ECP JAA 3.3557
58 6C8T EQJ 3.45745
59 6C92 EQJ 3.45745
60 6DND PLP 3.64964
61 1H74 ADP 3.71622
62 1H74 ILE 3.71622
63 4WXG 2BO 3.73832
64 3VP6 HLD 3.80313
65 5W70 9YM 3.82022
66 3ZRR PXG 3.90625
67 6HKE MLT 4.08805
68 6HKE LMR 4.08805
69 4BNU 9KQ 4.08922
70 1M32 PLP 4.09836
71 3GDH SAH 4.14938
72 1JGT APC 4.25056
73 1JGT CMA 4.25056
74 1OXO IK2 4.48878
75 2PO3 T4K 4.71698
76 1FC4 AKB PLP 4.73815
77 5OWC AYZ 4.91803
78 3PC3 P1T 4.9217
79 2F5X ASP 5.12821
80 1U08 PLP 5.18135
81 3RHC GSH 5.30973
82 6CD1 PLG 5.36913
83 6CD1 PLS 5.36913
84 2WK9 PLG 5.39846
85 2WK9 PLP 5.39846
86 2Q0L FAD 5.46624
87 3TLJ SAH 5.63003
88 2Z3Y F2N 5.81656
89 5TXR PLP 6.04027
90 2PW0 TRC 6.29723
91 4LNL 2BO 6.30631
92 4LNL 2BK 6.30631
93 4LNL PLG 6.30631
94 2UUU FAD 6.4877
95 1LC8 33P 6.59341
96 2P3V SRT 7.03125
97 1ZGS XMM 7.38255
98 3WGC PLG 8.21114
99 1JG3 ADN 8.51064
100 1XVB BHL 8.82353
101 5JBX MLI 9.1954
102 3OFK SAH 9.25926
103 6C2Z P1T 9.33333
104 2XBN PMP 9.36768
105 4ZSY RW2 9.61969
106 3GD8 GOL 9.86547
107 3B1J NAD 10.0295
108 4AZJ SEP PLP 10.2778
109 1DJ9 KAM 10.4167
110 4USQ FAD 10.5263
111 6D5H FV7 10.7784
112 6D59 FVJ 10.7784
113 6D56 FVM 10.7784
114 1ONI BEZ 11.5942
115 6C99 EQY 12.1212
116 1GS5 NLG 12.4031
117 1GS5 ANP 12.4031
118 5YSS NAD 12.8906
119 6MFL OPV 17.8571
120 2F5Z FAD 18.75
121 3PDB PMP 18.9526
122 3PD6 PMP 18.9526
123 5DDW 5B6 21.7002
124 6CBN OZY 26.484
125 5KGS 6SR 27.1335
126 3A8U PLP 27.9642
127 4RJD TFP 28.7879
128 2OAT PFM 29.1572
129 1ZC9 PMP 29.5612
130 4B98 PXG 29.7539
131 4UHO PLP 29.9776
132 2CJH AKG 30.5122
133 1MLY ACZ PLP 31.4685
134 6FYQ PLP 32.6446
135 5G4J EXT 33.1839
136 5WYF ILP 33.557
137 5YKT PMP 34.6756
138 4UOX PLP 35.123
139 5G09 6DF 35.123
140 4UOX PUT 35.123
141 4UOX PLP PUT 35.123
142 4ADC PLP 35.468
143 4BA5 PXG 37.3602
144 1SFF IK2 39.2019
Pocket No.: 2; Query (leader) PDB : 4ZM4; Ligand: PLP; Similar sites found with APoc: 57
This union binding pocket(no: 2) in the query (biounit: 4zm4.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 3CQ5 PMP 1.62602
2 2I3G NAP 1.70455
3 1K27 MTM 1.76678
4 4GN8 ASO 2.00669
5 3LKF PC 2.00669
6 2BJK NAD 2.01342
7 1BZL FAD 2.01342
8 4RSL FAD 2.02247
9 2R2N KYN 2.11765
10 2R2N PMP 2.11765
11 3OA2 NAD 2.20126
12 4WZ8 3W7 2.23714
13 1UU1 PMP HSA 2.38806
14 3QO8 SSA 2.47423
15 1MVQ MMA 2.54237
16 2VVT I24 2.75862
17 4KCT PYR 2.90828
18 6BKA FMN 2.94118
19 5IN3 G1P 2.99252
20 6GAS FAD 3.02115
21 4R8L ASP 3.11688
22 5IWQ PLP 3.22581
23 2HFK E4H 3.76176
24 2CJF RP4 3.82166
25 1ZK7 FAD 3.85439
26 2YI0 YI0 3.93013
27 4WOE 3S5 4.02685
28 4LWM MHO 4.14747
29 1K4M CIT 4.22535
30 5VEQ PMP 4.37956
31 2O3Z AI7 4.79705
32 4DYG MES 4.91803
33 3Q9T FAY 4.9217
34 5AE2 FAD 4.9217
35 5AE2 FYC 4.9217
36 5OD2 GLC 4.9217
37 1B8O IMH 5.28169
38 2ZYJ PGU 5.28967
39 1M7Y PPG 5.74713
40 2O1V ADP 5.81656
41 2HOX P1T 5.8548
42 4RKC PMP 6.03015
43 1WB4 SXX 6.06061
44 1SQL GUN 6.16438
45 4ZCC FAD 7.14286
46 3HRD FAD 8
47 1WYV PLP AOA 8.21918
48 4JSR 1NQ 8.77193
49 5C9P FUC 9.97375
50 6D5E FVG 10.7784
51 6D55 FWA 10.7784
52 6D5G FVD 10.7784
53 2X52 GYT 11.1111
54 3WMX THR 11.1732
55 4CE5 PDG 11.4114
56 3AXM 6PG 17.8295
57 4IJ6 SEP 24.1706
Pocket No.: 3; Query (leader) PDB : 4ZM4; Ligand: P3B; Similar sites found with APoc: 125
This union binding pocket(no: 3) in the query (biounit: 4zm4.bio3) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 6EWR PMP 1.40515
2 1E5F PLP 1.48515
3 9ABP GLA 1.63399
4 9ABP GAL 1.63399
5 5W19 9TD 1.78971
6 6CZY PMP 1.9337
7 3LKF PC 2.00669
8 1LW4 PLP 2.01729
9 1LW4 TLP 2.01729
10 3DR4 G4M 2.04604
11 3B8X G4M 2.05128
12 2R5E QLP 2.0979
13 2R5C C6P 2.0979
14 5K8B PDG 2.23325
15 5K6N XYP 2.23714
16 4ZAH T5K 2.27273
17 4HVK PMP 2.35602
18 1DFO PLG 2.39808
19 1AJS PLA 2.42718
20 1PMO PLR 2.46085
21 3QO8 SSA 2.47423
22 2FYF PLP 2.51256
23 2B99 RDL 2.5641
24 1RZM E4P 2.66272
25 4TQK NAG 2.70936
26 4C6H HE2 2.74914
27 1VJO PLP 2.79898
28 2X1E X1E 2.80112
29 3FIU POP 2.81124
30 1GCK ASP PLP 2.85714
31 2FAH MLA 2.90828
32 1JS3 PLP 142 2.90828
33 4REP FAD 2.90828
34 5W71 PLP 2.95455
35 5W71 9YM 2.95455
36 4E1O PLP PVH 3.13199
37 4K2M O1G 3.16027
38 3FRK TQP 3.21716
39 2Z9V PXM 3.31633
40 3QTP 2PG 3.40136
41 6C8T EQJ 3.45745
42 6DND PLP 3.64964
43 5LXB 7A9 3.71901
44 4WXG 2BO 3.73832
45 4NV0 MG7 3.76176
46 3VP6 HLD 3.80313
47 5W70 9YM 3.82022
48 3ZRR PXG 3.90625
49 1U1W 3HA 4.02685
50 5OSW DIU 4.02685
51 6HKE MLT 4.08805
52 6HKE LMR 4.08805
53 1M32 PLP 4.09836
54 4LWM MHO 4.14747
55 4I3G BGC 4.25056
56 5NCB JZ3 4.40098
57 1FC4 AKB PLP 4.73815
58 4UCF GLA 4.9217
59 3UB7 ACM 4.97238
60 2OVW CBI 5.10949
61 3RNM FAD 5.17241
62 1U08 PLP 5.18135
63 3RHC GSH 5.30973
64 6CD1 PLS 5.36913
65 6CD1 PLG 5.36913
66 2WG9 OCA 5.38462
67 2WK9 PLG 5.39846
68 2WK9 PLP 5.39846
69 5TXR PLP 6.04027
70 1SQL GUN 6.16438
71 4LNL PLG 6.30631
72 4LNL 2BO 6.30631
73 4LNL 2BK 6.30631
74 2HJR CIT 6.70732
75 6CI9 NAP 6.94981
76 3R9V DXC 6.99301
77 5ZI9 FLC 7.30769
78 1ZGS XMM 7.38255
79 4B3J COA 7.44417
80 1C3V PDC 7.7551
81 3WGC PLG 8.21114
82 4UYG 73B 8.28025
83 3N29 NSD 9.09091
84 5JBX MLI 9.1954
85 4ZSY RW2 9.61969
86 2GTE VA 9.67742
87 4ODT GP1 Z9M 9.81308
88 4AZJ SEP PLP 10.2778
89 2HJ9 AI2 10.4072
90 1DJ9 KAM 10.4167
91 5GUF CTP 10.4396
92 6BVM EBV 10.7784
93 6D55 FWA 10.7784
94 6D56 FVM 10.7784
95 1ONI BEZ 11.5942
96 1EP2 ORO 13.0268
97 6BE0 COA 15.894
98 3AXM 6PG 17.8295
99 2F5Z FAD 18.75
100 3PD6 PMP 18.9526
101 3PDB PMP 18.9526
102 5DDW 5B6 21.7002
103 3DXW ICC 25.885
104 6CBN OZY 26.484
105 5KGS 6SR 27.1335
106 3A8U PLP 27.9642
107 4RJD TFP 28.7879
108 2OAT PFM 29.1572
109 1ZC9 PMP 29.5612
110 4B98 PXG 29.7539
111 4UHO PLP 29.9776
112 2CJH AKG 30.5122
113 1MLY ACZ PLP 31.4685
114 6FYQ PLP 32.6446
115 5G4J EXT 33.1839
116 5WYF ILP 33.557
117 5YKT PMP 34.6756
118 4UOX PLP 35.123
119 4UOX PUT 35.123
120 4UOX PLP PUT 35.123
121 5G09 6DF 35.123
122 4ADC PLP 35.468
123 4BA5 PXG 37.3602
124 2VOH CIT 38.4615
125 1SFF IK2 39.2019
Pocket No.: 4; Query (leader) PDB : 4ZM4; Ligand: PLP; Similar sites found with APoc: 20
This union binding pocket(no: 4) in the query (biounit: 4zm4.bio3) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3IAE D7K 1.78971
2 4UP3 FAD 1.91083
3 5X20 AOT 1.92308
4 5U5N NAD 2.15054
5 3LZW FAD 2.40964
6 2Q1W NAD 3.003
7 2VYN NAD 3.02115
8 2WET FAD 3.13199
9 2C6Q IMP 3.1339
10 2C6Q NDP 3.1339
11 4DPL NAP 4.17827
12 5UQW GDP 4.2328
13 6H3O FAD 4.25056
14 2E5V FAD 4.47427
15 4NJH SAM 6.95652
16 4NJH 2K8 6.95652
17 2PS1 PRP 10.177
18 6D5M FW4 10.7784
19 6D5J FV4 10.7784
20 6D5L FW7 10.7784
Pocket No.: 5; Query (leader) PDB : 4ZM4; Ligand: P3B; Similar sites found with APoc: 20
This union binding pocket(no: 5) in the query (biounit: 4zm4.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 2OO0 PLP 1.34228
2 1B4N GUA 1.78971
3 2X41 BGC 2.46085
4 2HIM ASN 2.7933
5 3BY8 MLT 2.8169
6 5MB4 NAG 2.99252
7 3OO6 GAL 3.13253
8 3WCZ CIT 3.24675
9 5E5U MLI 3.40909
10 1QFT HSM 3.42857
11 6C92 EQJ 3.45745
12 4BNU 9KQ 4.08922
13 5U8U FAD 4.47427
14 5J60 FAD 4.6875
15 3CQO FUC 5.46075
16 2IMP LAC 8.50112
17 3CL7 HYN 8.76623
18 6BVK EAV 10.7784
19 1EP2 FMN 13.0268
20 5N6N SUC 19.5833
Pocket No.: 6; Query (leader) PDB : 4ZM4; Ligand: PLP; Similar sites found with APoc: 8
This union binding pocket(no: 6) in the query (biounit: 4zm4.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1CL2 PPG 1.26582
2 3ITJ FAD 1.47929
3 5XFV FMN 2.09581
4 3A06 FOM 2.92553
5 3VC3 C6P 3.19767
6 4XDA RIB 4.53074
7 1G51 AMO 6.04027
8 1O94 ADP 8.75
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