Receptor
PDB id Resolution Class Description Source Keywords
1DJ9 2 Å EC: 2.3.1.47 CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KET 8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND P RODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BI OSYNTHETIC PATHWAY. ESCHERICHIA COLI 8-AMINO-7-OXONONANOATE SYNTHASE BIOTIN PYRIDOXAL-5-prime -PHOSPHTRANSFERASE
Ref.: MECHANISM OF 8-AMINO-7-OXONONANOATE SYNTHASE: SPECT KINETIC, AND CRYSTALLOGRAPHIC STUDIES. BIOCHEMISTRY V. 39 516 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
KAM A:400;
Valid;
none;
submit data
418.379 C17 H27 N2 O8 P Cc1c(...
MG A:500;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
SO4 A:401;
A:402;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1DJ9 2 Å EC: 2.3.1.47 CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KET 8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND P RODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BI OSYNTHETIC PATHWAY. ESCHERICHIA COLI 8-AMINO-7-OXONONANOATE SYNTHASE BIOTIN PYRIDOXAL-5-prime -PHOSPHTRANSFERASE
Ref.: MECHANISM OF 8-AMINO-7-OXONONANOATE SYNTHASE: SPECT KINETIC, AND CRYSTALLOGRAPHIC STUDIES. BIOCHEMISTRY V. 39 516 2000
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1DJ9 - KAM C17 H27 N2 O8 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 1 families.
1 1DJ9 - KAM C17 H27 N2 O8 P Cc1c(c(c(c....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1DJ9 - KAM C17 H27 N2 O8 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: KAM; Similar ligands found: 51
No: Ligand ECFP6 Tc MDL keys Tc
1 KAM 1 1
2 PDD 0.68 0.904762
3 PP3 0.68 0.904762
4 PDA 0.68 0.904762
5 N5F 0.626506 0.9375
6 PGU 0.609756 0.921875
7 PDG 0.609756 0.921875
8 2BK 0.6 0.875
9 TLP 0.6 0.875
10 2BO 0.6 0.875
11 PLG 0.597403 0.890625
12 76U 0.595238 0.907692
13 PPD 0.592593 0.890625
14 ILP 0.590361 0.876923
15 PY5 0.585366 0.893939
16 PLS 0.580247 0.861538
17 IN5 0.576923 0.873016
18 PY6 0.576471 0.924242
19 C6P 0.573171 0.861538
20 QLP 0.564706 0.867647
21 7XF 0.552941 0.892308
22 ORX 0.551724 0.907692
23 PL4 0.550562 0.907692
24 PE1 0.545455 0.907692
25 P1T 0.536585 0.823529
26 EA5 0.534091 0.880597
27 IK2 0.53012 0.850746
28 PLA 0.529412 0.893939
29 PMG 0.528736 0.924242
30 AQ3 0.515789 0.811594
31 5PA 0.505882 0.850746
32 CBA 0.5 0.808824
33 33P 0.494118 0.859375
34 HEY 0.488889 0.893939
35 3LM 0.483516 0.814286
36 PSZ 0.483516 0.774648
37 PXP 0.473684 0.761905
38 PLP ALO 0.471264 0.830769
39 PL2 0.461538 0.811594
40 PMH 0.454545 0.658228
41 RW2 0.452632 0.826087
42 PXG 0.452632 0.833333
43 PMP 0.448718 0.825397
44 GT1 0.443038 0.712121
45 7TS 0.434783 0.666667
46 DCS 0.430108 0.696203
47 PL8 0.418367 0.783784
48 9YM 0.416667 0.757143
49 7B9 0.41 0.816901
50 PL6 0.408602 0.784615
51 PLP 2KZ 0.402174 0.80303
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1DJ9; Ligand: KAM; Similar sites found: 105
This union binding pocket(no: 1) in the query (biounit: 1dj9.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1PMO PLR 0.001104 0.42737 1.30208
2 1B9I PXG 0.0002204 0.48315 1.5625
3 2HOX P1T 0.000978 0.44562 1.5625
4 3ZRR PXG 0.0004205 0.46426 1.82292
5 4BA5 PXG 0.0003754 0.45953 1.82292
6 1LC8 33P 0.00004292 0.52172 1.92308
7 5GVL PLG 0.00001198 0.56748 2.08333
8 5GVL GI8 0.00001198 0.56748 2.08333
9 3E2Y PMP 0.00007443 0.4783 2.08333
10 4FL0 PLP 0.001428 0.42457 2.08333
11 4ZSY RW2 0.0004772 0.42668 2.34375
12 5IWQ PLP 0.00382 0.42331 2.34375
13 3FRK TQP 0.002275 0.44724 2.41287
14 5KGS 6SR 0.001853 0.46529 2.60417
15 2X5F PLP 0.000548 0.43498 2.60417
16 5DDW 5B6 0.001943 0.40033 2.60417
17 1VJO PLP 0.0007819 0.44542 2.86458
18 1MLY ACZ PLP 0.002199 0.42982 2.86458
19 3BS8 PMP 0.0013 0.42377 2.86458
20 4WXG 2BO 0.00001018 0.47159 3.03738
21 2ZYJ PGU 0.0002816 0.48373 3.125
22 1GCK ASP PLP 0.0003049 0.47056 3.125
23 3WGC PLG 0.00002704 0.51012 3.22581
24 2FYF PLP 0.0006121 0.42478 3.26633
25 4LNL 2BO 0.00002975 0.50827 3.3033
26 4LNL PLG 0.00002513 0.50411 3.3033
27 3PDB PMP 0.00008119 0.47595 3.38542
28 3PD6 PMP 0.00006361 0.47331 3.38542
29 5U23 TQP 0.0009436 0.46532 3.38542
30 4RKC PMP 0.0006112 0.45508 3.38542
31 4AOA IK2 0.0007776 0.44552 3.38542
32 1JS3 PLP 142 0.002622 0.4264 3.38542
33 4M2K PLP 0.000145 0.45411 3.64583
34 1E5F PLP 0.0001466 0.47761 3.90625
35 4JE5 PMP 0.001587 0.44609 3.90625
36 4JE5 PLP 0.001681 0.44489 3.90625
37 3LL5 IPE 0.02197 0.4038 4.01606
38 4HVK PMP 0.00007995 0.46036 4.18848
39 2R2N PMP 0.0003319 0.47261 4.42708
40 2TPL HPP 0.0008185 0.46051 4.42708
41 4E1O PLP PVH 0.005752 0.41648 4.42708
42 4AZJ SEP PLP 0.001144 0.44662 4.44444
43 5DHU 5A8 0.0401 0.40726 4.77941
44 2X5D PLP 0.0006217 0.41176 4.85437
45 1M7Y PPG 0.0004779 0.4778 4.94792
46 4E3Q PMP 0.000178 0.45489 4.94792
47 1SFF IK2 0.001918 0.4345 4.94792
48 2Z9V PXM 0.0005845 0.42407 4.94792
49 3EI9 PL6 0.0006577 0.4107 4.94792
50 1AJS PLA 0.0004772 0.46776 5.20833
51 3BWN PMP PHE 0.001181 0.44599 5.20833
52 3BWN PMP 0.0004745 0.44418 5.20833
53 1T9D FAD 0.03125 0.40214 5.20833
54 3VP6 HLD 0.0007022 0.46187 5.46875
55 1C7O PPG 0.008778 0.40464 5.46875
56 1LW4 TLP 0.0001044 0.4892 5.4755
57 1LW4 PLP 0.00008171 0.48885 5.4755
58 2OGA PGU 0.001901 0.43661 5.72917
59 5W70 9YM 0.00003436 0.51333 5.8427
60 1ELU PDA 0.001574 0.43635 5.98958
61 5ECP MET 0.03308 0.40092 6.27803
62 4UHO PLP 0.003414 0.44047 7.03125
63 5W71 9YM 0.0005001 0.48993 7.29167
64 5W71 PLP 0.0001515 0.47952 7.29167
65 1U08 PLP 0.00022 0.45072 7.55208
66 2ZC0 PMP 0.00004099 0.50483 7.8125
67 3CQ5 PMP 0.00006461 0.45672 7.85908
68 3B8X G4M 0.0005288 0.48138 8.07292
69 2R5C C6P 0.0001501 0.48444 8.33333
70 2R5E QLP 0.0002169 0.47723 8.33333
71 5DJ3 5DK 0.0004684 0.45996 8.51064
72 5X2Z 3LM 0.00005102 0.51632 8.59375
73 5X30 7XF 0.00004386 0.48249 8.59375
74 5X30 4LM 0.0001001 0.47593 8.59375
75 2CJH AKG 0.007704 0.40136 9.89583
76 4K2M O1G 0.001114 0.44905 10.1562
77 4ZM4 PLP 0.0005258 0.45805 10.4167
78 1DFO PLG 0.000008405 0.54093 10.6771
79 5WYF ILP 0.0002397 0.47527 11.1979
80 1GEX PLP HSA 0.0005648 0.46798 11.236
81 4ADC PLP 0.001748 0.4391 13.5417
82 1GDE GLU PLP 0.002414 0.42801 13.5417
83 2PO3 T4K 0.002217 0.45161 13.8021
84 1ZC9 PMP 0.00111 0.44315 13.8021
85 4R5Z PMP 0.0001472 0.43891 14.5833
86 4R5Z SIN 0.0002293 0.404 14.5833
87 4IY7 KOU 0.0001931 0.4795 14.8438
88 4IYO 0JO 0.0001972 0.47909 14.8438
89 4IY7 0JO 0.000209 0.47796 14.8438
90 1MDZ DCS 0.0009614 0.46767 15.1042
91 1MDZ PLP 0.0009007 0.46767 15.1042
92 1CL2 PPG 0.0009877 0.44752 15.625
93 3DR4 G4M 0.001142 0.47022 15.8854
94 2FNU PMP UD1 0.0005972 0.48143 16
95 1WYV PLP AOA 0.002314 0.42673 16.895
96 3FQ8 PMP 0.001543 0.44438 18.75
97 5G09 6DF 0.001755 0.43625 19.0104
98 5K8B PDG 0.00006779 0.50452 20.5729
99 4UOX PLP 0.001747 0.41778 21.3542
100 4UOX PUT 0.007982 0.40068 21.3542
101 1UU1 PMP HSA 0.0001994 0.48105 22.9851
102 4B98 PXG 0.004136 0.41548 29.6875
103 2WK9 PLG 0.000000002407 0.73213 40.625
104 2WK9 PLP 0.00000001667 0.68772 40.625
105 2XBN PMP 0.00000003599 0.66223 46.3542
106 1FC4 AKB PLP 0.0000005713 0.59065 50
Pocket No.: 2; Query (leader) PDB : 1DJ9; Ligand: KAM; Similar sites found: 134
This union binding pocket(no: 2) in the query (biounit: 1dj9.bio2) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO4 PIH 0.003545 0.47154 None
2 3S9K CIT 0.0179 0.44858 1.04167
3 1PEA ACM 0.004593 0.44896 1.5625
4 1Q11 TYE 0.01285 0.4049 1.6129
5 3TKA CTN 0.002125 0.49373 1.72911
6 2BOI MFU 0.003741 0.4278 1.76991
7 2ZJ5 ADP 0.005788 0.42507 1.82292
8 3TFC PEP 0.01058 0.40851 1.82292
9 3AYS CT3 0.008655 0.40305 1.8617
10 2ZWS PLM 0.00984 0.45684 2.08333
11 4NAO AKG 0.01292 0.42059 2.08333
12 1H0C AOA 0.01663 0.41538 2.08333
13 1O68 KIV 0.001848 0.44085 2.18182
14 1FW1 GSH 0.004094 0.40723 2.31481
15 3CEV ARG 0.01281 0.40044 2.34114
16 2Q8H TF4 0.02682 0.41736 2.34375
17 2WQF FMN 0.004974 0.40824 2.47525
18 2HFK E4H 0.007544 0.4148 2.50784
19 4PPU TYR 0.009182 0.41115 2.51799
20 3GTD MLI 0.002898 0.43831 2.60417
21 3I0O SMI 0.007695 0.4196 2.65487
22 4LWM MHO 0.03735 0.42322 2.76498
23 1T10 F6P 0.001002 0.45862 2.86458
24 4M5P MLA 0.01062 0.44602 2.86458
25 1MVN PCO 0.004877 0.40836 2.87081
26 1Z44 NPO 0.01899 0.44074 2.95858
27 1I0Z OXM 0.003071 0.46574 3.003
28 2BZ1 TAU 0.03043 0.42914 3.06122
29 3R51 MMA 0.004696 0.45629 3.125
30 2XDQ MGX 0.007871 0.44479 3.125
31 2YIV YIV 0.018 0.4197 3.125
32 2YIV NBN 0.02872 0.40403 3.125
33 3LTW HLZ 0.007973 0.42449 3.21429
34 3E5P PPI 0.01017 0.46048 3.2345
35 4LNL 2BK 0.0000003205 0.46382 3.3033
36 3BHO B4P 0.04168 0.41394 3.36538
37 2EB5 OXL 0.001381 0.45923 3.37079
38 3MD0 GDP 0.002727 0.42823 3.38028
39 2IZ1 ATR 0.00876 0.42262 3.38542
40 3L24 GOA 0.02735 0.41692 3.38542
41 1KTC NGA 0.01314 0.40448 3.38542
42 4LHM AZZ 0.01819 0.40306 3.38542
43 1SC3 MLI 0.0141 0.42495 3.40909
44 4LIT AKG 0.004128 0.43154 3.4398
45 3D2Y AH0 ALA FGA LYS 0.002885 0.40093 3.44828
46 2WGC SIA GAL BGC 0.002878 0.48681 3.50877
47 1WGC SIA GAL BGC 0.007145 0.45524 3.50877
48 4RJK PYR 0.008394 0.43607 3.64583
49 1QH9 LAC 0.01483 0.41215 3.64583
50 2Q09 DI6 0.01246 0.40093 3.64583
51 2QLX RM4 0.01805 0.41368 3.7037
52 3ZUY TCH 0.008373 0.40363 3.71517
53 3P7I P7I 0.005539 0.42052 3.73832
54 1JN2 SFP 0.0002096 0.57204 3.79747
55 3U1T MLI 0.0117 0.42264 3.8835
56 4WBD ADP 0.01995 0.4116 3.90625
57 9LDT OXM 0.002668 0.47814 3.91566
58 3LZW NAP 0.008543 0.40087 3.91566
59 4B16 NAG 0.02807 0.42327 4.13534
60 2VAR AMP 0.006236 0.40876 4.15335
61 3ZF8 GDP 0.00466 0.41383 4.16667
62 1DBT U5P 0.002829 0.40123 4.1841
63 1RYI GOA 0.04292 0.41588 4.18848
64 3QDY A2G GAL 0.02233 0.41507 4.1958
65 3QDT A2G GAL 0.02575 0.41199 4.1958
66 3QDY CBS 0.03087 0.40254 4.1958
67 1V6A TRE 0.008624 0.41742 4.21687
68 2Y6P CTP 0.009583 0.40127 4.2735
69 4IXW IXW 0.004663 0.41861 4.33071
70 1C1L GAL BGC 0.03184 0.40189 4.37956
71 2VQ5 HBA 0.009305 0.42736 4.47761
72 2VQ5 LDP 0.0196 0.4244 4.47761
73 1WRA PC 0.02688 0.40541 4.54545
74 1W3R PYR 0.0105 0.43127 4.62963
75 3JQ3 ADP 0.01027 0.40006 4.64481
76 4C6F NCD 0.001787 0.43051 4.6875
77 4C6F DOR 0.001787 0.43051 4.6875
78 1O9U ADZ 0.01142 0.43648 4.85714
79 2P69 PLP 0.009855 0.41485 4.90196
80 1Y1A GSH 0.01861 0.44068 4.91803
81 3R6K FUC GAL GLA 0.0153 0.4171 4.91803
82 1Y7P RIP 0.01488 0.42379 4.93274
83 2V5E SCR 0.008466 0.45129 4.9505
84 3GJB AKG 0.007178 0.41086 5.01567
85 2Q1A 2KT 0.01188 0.41655 5.11945
86 1NU4 MLA 0.01635 0.43595 5.15464
87 4W6Z ETF 0.01766 0.42673 5.18732
88 2JFV FLC 0.01294 0.41487 5.20833
89 2JGS BTN 0.004023 0.42919 5.38462
90 4JCA CIT 0.009832 0.44781 5.38922
91 4O8A 2OP 0.00163 0.47981 5.46875
92 3BY8 MLT 0.01454 0.41815 5.6338
93 1BTN I3P 0.02965 0.43033 5.66038
94 1H16 DTL 0.004465 0.45741 5.72917
95 1H16 PYR 0.01348 0.42592 5.72917
96 5XHA FRU FRU 0.007487 0.40558 5.72917
97 1YRX FMN 0.005477 0.40246 5.78512
98 1UW1 ADP 0.01255 0.41021 6.25
99 2JC9 ADN 0.01207 0.40606 6.25
100 1ULE GLA GAL NAG 0.009261 0.43397 6.66667
101 1TOI HCI 0.000006472 0.47356 6.77083
102 3SQG COM 0.01537 0.43738 6.81004
103 3NNF AKG 0.01593 0.41072 6.97674
104 2Q37 3AL 0.009041 0.41651 7.29167
105 4EXO PYR 0.006514 0.44149 7.53425
106 1YOA FMN 0.003279 0.48363 7.54717
107 2Y7P SAL 0.002517 0.43514 7.79817
108 1XE7 GUN 0.01897 0.42513 7.88177
109 4GO7 THR 0.003961 0.41667 8.5
110 2YLD CMO 0.006511 0.42851 8.66142
111 1Y2W NAG 0.01827 0.40798 8.85417
112 2O66 FLC 0.01018 0.41424 8.88889
113 1ZZ7 S0H 0.0111 0.40763 9.09091
114 2OFE NAG 0.01654 0.40997 9.15493
115 3L6R MLI 0.009954 0.42597 9.53757
116 1XX4 BAM 0.006075 0.45056 9.57854
117 1ZJ6 G3D 0.002427 0.42036 9.62567
118 2WCI GSH 0.008318 0.41811 9.62963
119 1H2M OGA 0.01181 0.41668 9.89583
120 3P3N AKG 0.01327 0.41436 9.89583
121 2WA4 069 0.006132 0.4047 9.89583
122 1SS4 GSH 0.01331 0.45312 10.4575
123 1SS4 CIT 0.04279 0.448 10.4575
124 4LO6 SIA GAL 0.002263 0.46016 10.5263
125 4COQ SAN 0.01845 0.40779 10.5263
126 3F81 STT 0.02946 0.41524 11.4754
127 4F8L GAL 0.00948 0.45775 12.4138
128 1LYX PGA 0.0008646 0.43273 12.5
129 2FYU FDN 0.002699 0.40194 15.3846
130 3CF6 SP1 0.001947 0.41502 17.7083
131 3UEC ALA ARG TPO LYS 0.01832 0.41336 18.4932
132 1TUV VK3 0.04905 0.4037 19.2982
133 1ECM TSA 0.002636 0.42884 24.7706
134 1T0S BML 0.003058 0.45764 25.5814
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