Receptor
PDB id Resolution Class Description Source Keywords
4K2M 1.71 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF NTDA FROM BACILLUS SUBTILIS IN COMPLEX PLP EXTERNAL ALDIMINE ADDUCT WITH KANOSAMINE-6-PHOSPHATE BACILLUS SUBTILIS SUBSP. SUBTILIS SUGAR AMINOTRANSFERASE ASPERTATE AMINOTRANSFERASE FOLD HOMADDITIONAL N-TERNINAL DOMAIN 3-KETO-GLUCOSE-6-PHOSPHATE AMINITRANSFERASE KANOSAMINE-6-PHOSPHATE TRANSFERASE
Ref.: THE STRUCTURE OF NTDA, A SUGAR AMINOTRANSFERASE INV THE KANOSAMINE BIOSYNTHETIC PATHWAY IN BACILLUS SUB REVEALS A NEW SUBCLASS OF AMINOTRANSFERASES. J.BIOL.CHEM. V. 288 34121 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO B:502;
B:506;
B:505;
A:506;
A:505;
A:502;
A:503;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
ACT B:504;
A:504;
B:503;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
O1G A:501;
B:501;
Valid;
Valid;
none;
none;
submit data
488.278 C14 H22 N2 O13 P2 Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4K2M 1.71 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF NTDA FROM BACILLUS SUBTILIS IN COMPLEX PLP EXTERNAL ALDIMINE ADDUCT WITH KANOSAMINE-6-PHOSPHATE BACILLUS SUBTILIS SUBSP. SUBTILIS SUGAR AMINOTRANSFERASE ASPERTATE AMINOTRANSFERASE FOLD HOMADDITIONAL N-TERNINAL DOMAIN 3-KETO-GLUCOSE-6-PHOSPHATE AMINITRANSFERASE KANOSAMINE-6-PHOSPHATE TRANSFERASE
Ref.: THE STRUCTURE OF NTDA, A SUGAR AMINOTRANSFERASE INV THE KANOSAMINE BIOSYNTHETIC PATHWAY IN BACILLUS SUB REVEALS A NEW SUBCLASS OF AMINOTRANSFERASES. J.BIOL.CHEM. V. 288 34121 2013
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 4K2M - O1G C14 H22 N2 O13 P2 Cc1c(c(c(c....
2 4K2I - PMP C8 H13 N2 O5 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 1068 families.
1 4K2M - O1G C14 H22 N2 O13 P2 Cc1c(c(c(c....
2 4K2I - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 4K2M - O1G C14 H22 N2 O13 P2 Cc1c(c(c(c....
2 4K2I - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: O1G; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 O1G 1 1
2 MPM 0.494118 0.761905
3 KOU 0.488372 0.83871
4 TQP 0.483871 0.707317
5 7SG 0.483871 0.707317
6 HCP 0.482759 0.753846
7 EPC 0.481928 0.8
8 EXT 0.47619 0.806452
9 0JO 0.465116 0.753846
10 4LM 0.465116 0.765625
11 T5K 0.456693 0.719512
12 T4K 0.456693 0.719512
13 PLP 0.454545 0.75
14 PL6 0.450549 0.793651
15 6DF 0.450549 0.786885
16 P3D 0.449438 0.695652
17 PZP 0.448718 0.783333
18 PUS 0.4375 0.722222
19 PL5 0.4375 0.757576
20 4RA 0.43609 0.776316
21 Z98 0.430108 0.761194
22 5DK 0.424242 0.714286
23 UD0 0.419118 0.766234
24 AN7 0.413793 0.754098
25 FOO 0.409091 0.790323
26 LLP 0.408163 0.75
27 P89 0.4 0.728571
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4K2M; Ligand: O1G; Similar sites found: 86
This union binding pocket(no: 1) in the query (biounit: 4k2m.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4B98 PXG 0.001347 0.40898 1.3544
2 1MLY ACZ PLP 0.0009855 0.41787 1.6317
3 1FC4 AKB PLP 0.0009204 0.42219 1.99501
4 5KGS 6SR 0.0009075 0.46 2.0316
5 1M7Y PPG 0.009726 0.40023 2.06897
6 1GEX PLP HSA 0.005026 0.40682 2.24719
7 4UOX PLP 0.0001014 0.50836 2.25734
8 4UOX PUT 0.0008436 0.45456 2.25734
9 4UOX PLP PUT 0.001848 0.43482 2.25734
10 2XBN PMP 0.006238 0.40289 2.34192
11 5G4J EXT 0.001563 0.41031 2.48307
12 4E3Q PMP 0.00008928 0.42831 2.7088
13 1VJO PLP 0.0004399 0.46747 2.79898
14 4ZM4 PLP 0.000143 0.43392 3.16027
15 4ZM4 P3B 0.001192 0.41905 3.16027
16 3ZRR PXG 0.0004874 0.43504 3.38542
17 4ZSY RW2 0.0005746 0.43658 3.61174
18 1KA1 A3P 0.01547 0.40024 3.64146
19 3WGC PLG 0.0001401 0.43802 3.81232
20 3JYY PPV 0.02917 0.40568 4.18118
21 3PDB PMP 0.00003404 0.45206 4.2394
22 3PD6 PMP 0.00008309 0.43285 4.2394
23 4BA5 PXG 0.0001113 0.4947 4.28894
24 2ZYJ PGU 0.006236 0.40437 4.53401
25 3FQ8 PMP 0.0005028 0.44504 4.68384
26 2R2N PMP 0.0003518 0.48255 4.70588
27 1AJS PLA 0.000184 0.46309 4.85437
28 3BWN PMP 0.0003786 0.41801 4.85933
29 3BWN PMP PHE 0.003602 0.4046 4.85933
30 1M32 PLP 0.003007 0.45512 4.91803
31 2ZC0 PMP 0.0001534 0.48307 5.15971
32 1DFO PLG 0.0007072 0.4282 5.51559
33 2WK9 PLG 0.0004459 0.46024 5.9126
34 2WK9 PLP 0.0006224 0.45114 5.9126
35 4RKC PMP 0.0002517 0.42936 6.03015
36 4AOA IK2 0.0001636 0.43429 6.09481
37 5GVL PLG 0.004073 0.42694 6.33484
38 5GVL GI8 0.004073 0.42694 6.33484
39 2Z9V PXM 0.0001198 0.52526 6.37755
40 2CJH AKG 0.0003771 0.47052 6.77201
41 3BS8 PMP 0.0003619 0.41056 7.07763
42 1LC8 33P 0.0003713 0.42474 7.41758
43 2FYF PLP 0.006375 0.43132 8.12641
44 4R5Z PMP 0.002799 0.41247 9.26431
45 3OPT AKG 0.03283 0.40099 9.65147
46 4ADC PLP 0.001167 0.42992 9.85222
47 1ZC9 PMP 0.0002153 0.44114 9.93072
48 5G09 6DF 0.0008198 0.42584 9.93228
49 4IY7 KOU 0.002209 0.42369 10.0756
50 4IY7 0JO 0.002472 0.4216 10.0756
51 4IYO 0JO 0.002395 0.40776 10.0756
52 1DJ9 KAM 0.001114 0.44905 10.1562
53 5WYF ILP 0.0009228 0.42337 10.158
54 1E5F PLP 0.0001949 0.43814 10.6436
55 4WXG 2BO 0.001216 0.42918 10.7477
56 3E2Y PMP 0.0003912 0.41644 11.2195
57 1SFF IK2 0.000284 0.44335 11.9718
58 1GCK ASP PLP 0.001268 0.43402 12.4675
59 1U08 PLP 0.000202 0.41635 12.9534
60 2R5E QLP 0.002595 0.40704 13.0536
61 2R5C C6P 0.002913 0.40513 13.0536
62 1XI9 PLP 0.02436 0.40191 14.2857
63 3VP6 HLD 0.0007211 0.44036 14.6727
64 5X2Z 3LM 0.001582 0.42783 15.0754
65 5X30 7XF 0.0008133 0.42309 15.0754
66 5X30 4LM 0.0007829 0.41837 15.0754
67 2OAT PFM 0.002171 0.4002 17.5399
68 4JE5 PLP 0.01508 0.40832 23.9278
69 4JE5 PMP 0.01669 0.40614 23.9278
70 4LNL PLG 0.000142 0.42849 26.4264
71 4LNL 2BO 0.0002792 0.42584 26.4264
72 1LW4 TLP 0.0003294 0.4346 28.8184
73 1LW4 PLP 0.0002055 0.43029 28.8184
74 5K8B PDG 0.0000000001111 0.7167 29.5285
75 1O69 X04 0.00000003209 0.43913 29.9492
76 3B8X G4M 0.000000005065 0.67698 37.9487
77 2PO3 T4K 0.000000001369 0.55514 38.2075
78 5W71 9YM 0.000000001179 0.71689 39.5455
79 5W71 PLP 0.00000000001096 0.70551 39.5455
80 2FNU PMP UD1 0.0000000004083 0.72884 41.8667
81 4ZAH T5K 0.0000000007187 0.61852 43.1818
82 1MDZ DCS 0.0003749 0.49777 48.0916
83 1MDZ PLP 0.0003497 0.49777 48.0916
84 3DR4 G4M 0.0000000042 0.51121 48.3376
85 2OGA PGU 0.0000000006133 0.67543 49.6241
86 5U23 TQP 0.0000000003219 0.72139 49.7382
Pocket No.: 2; Query (leader) PDB : 4K2M; Ligand: O1G; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4k2m.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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