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Receptor
PDB id Resolution Class Description Source Keywords
1NJJ 2.45 Å EC: 4.1.1.17 CRYSTAL STRUCTURE DETERMINATION OF T. BRUCEI ORNITHINE DECAR BOUND TO D-ORNITHINE AND TO G418 TRYPANOSOMA BRUCEI GAMBIENSE ORNITHINE DECARBOXYLASE ODC PLP PYRIDOXAL 5-prime -PHOSPHATE DORNITHINE G418 LYASE
Ref.: X-RAY STRUCTURE DETERMINATION OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE BOUND TO D-ORNITHINE AND TO INSIGHTS INTO SUBSTRATE BINDING AND ODC CONFORMATIO FLEXIBILITY. J.BIOL.CHEM. V. 278 22037 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GET A:601;
B:602;
C:603;
Valid;
Valid;
Valid;
none;
none;
none;
Ki = 8 mM
496.552 C20 H40 N4 O10 C[C@H...
ORX A:602;
B:603;
C:604;
D:426;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 0.27 mM
363.303 C13 H22 N3 O7 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1NJJ 2.45 Å EC: 4.1.1.17 CRYSTAL STRUCTURE DETERMINATION OF T. BRUCEI ORNITHINE DECAR BOUND TO D-ORNITHINE AND TO G418 TRYPANOSOMA BRUCEI GAMBIENSE ORNITHINE DECARBOXYLASE ODC PLP PYRIDOXAL 5-prime -PHOSPHATE DORNITHINE G418 LYASE
Ref.: X-RAY STRUCTURE DETERMINATION OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE BOUND TO D-ORNITHINE AND TO INSIGHTS INTO SUBSTRATE BINDING AND ODC CONFORMATIO FLEXIBILITY. J.BIOL.CHEM. V. 278 22037 2003
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1NJJ Ki = 8 mM GET C20 H40 N4 O10 C[C@H]([C@....
2 1F3T - PLP PUT n/a n/a
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1NJJ Ki = 8 mM GET C20 H40 N4 O10 C[C@H]([C@....
2 1F3T - PLP PUT n/a n/a
3 2OO0 Kd = 0.05 uM PLP C8 H10 N O6 P Cc1c(c(c(c....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2NVA - PL2 C13 H24 N5 O5 P [H]/N=C(/N....
2 2NV9 - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 1NJJ Ki = 8 mM GET C20 H40 N4 O10 C[C@H]([C@....
4 1F3T - PLP PUT n/a n/a
5 2OO0 Kd = 0.05 uM PLP C8 H10 N O6 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GET; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 GET 1 1
2 827 0.679012 0.943396
3 51G 0.586207 0.943396
4 LLL 0.563218 0.875
5 SIS 0.563218 0.859649
6 DVM 0.45098 0.819672
Ligand no: 2; Ligand: ORX; Similar ligands found: 63
No: Ligand ECFP6 Tc MDL keys Tc
1 ORX 1 1
2 PE1 0.898551 1
3 PY6 0.816901 0.924242
4 N5F 0.805556 0.968254
5 PL4 0.797297 1
6 PY5 0.785714 0.923077
7 QLP 0.777778 0.924242
8 PDG 0.763889 0.952381
9 PGU 0.763889 0.952381
10 7XF 0.763889 0.952381
11 LPI 0.753425 0.882353
12 PLS 0.732394 0.920635
13 C6P 0.722222 0.920635
14 PPD 0.722222 0.920635
15 ILP 0.671053 0.876923
16 2BK 0.662162 0.875
17 2BO 0.662162 0.875
18 TLP 0.662162 0.875
19 PDD 0.657534 0.875
20 PDA 0.657534 0.875
21 PP3 0.657534 0.875
22 AQ3 0.597701 0.865672
23 IN5 0.594595 0.84375
24 76U 0.592593 0.907692
25 PLG 0.573333 0.890625
26 EA5 0.566265 0.938462
27 KAM 0.551724 0.907692
28 P1T 0.551282 0.878788
29 CBA 0.548781 0.835821
30 IK2 0.544304 0.850746
31 5PA 0.5375 0.907692
32 33P 0.525 0.80303
33 PLA 0.52439 0.865672
34 PMP 0.521127 0.854839
35 PMG 0.505882 0.895522
36 PL2 0.505882 0.865672
37 HEY 0.5 0.893939
38 3LM 0.494253 0.814286
39 PSZ 0.494253 0.774648
40 PXP 0.486111 0.761905
41 PMH 0.481928 0.679487
42 RW2 0.477778 0.852941
43 PXG 0.477778 0.833333
44 GT1 0.472973 0.686567
45 DCS 0.471264 0.74026
46 7TS 0.45977 0.6875
47 PPE 0.45977 0.9375
48 9YM 0.455556 0.835821
49 PL8 0.44086 0.808219
50 PPG 0.44086 0.878788
51 7B9 0.431579 0.842857
52 Z98 0.426966 0.861538
53 LLP 0.419355 0.90625
54 P3D 0.413793 0.875
55 PLR 0.410959 0.671875
56 PLP 2KZ 0.409091 0.80303
57 F0G 0.406977 0.738462
58 5DK 0.40625 0.863636
59 EQJ 0.40625 0.863636
60 PL5 0.404255 0.859375
61 CAN PLP 0.404255 0.880597
62 KOU 0.402299 0.8
63 PL6 0.4 0.784615
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1NJJ; Ligand: GET; Similar sites found with APoc: 34
This union binding pocket(no: 1) in the query (biounit: 1njj.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5VKM GAL SIA 1.54321
2 4HWS 1B3 1.94647
3 4WGF HX2 1.95122
4 4CSD MFU 2.20588
5 5N9T 8QQ 2.2409
6 5AOV NAP 2.38095
7 6DEF GCP 2.55754
8 2YC5 6BC 2.63158
9 5CDH TLA 2.67857
10 2NU8 COA 3.125
11 3IAE D7K 3.29412
12 6F7X MFU 3.33333
13 2BS5 BGC GAL FUC 3.33333
14 4TVD BGC 3.52941
15 2DBZ NAP 3.89222
16 3ZW2 GAL FUC 4.5977
17 3ZW2 NAG GAL FUC 4.5977
18 4O08 PO6 4.6729
19 2H8Z 8CM 5.29248
20 3A5Z KAA 5.75916
21 5N26 CPT 6.04396
22 4X3R 686 6.11765
23 2GGX NPJ 7.5
24 3UG4 AHR 7.52941
25 4D4U FUC NDG GAL FUC 7.61905
26 4O4F ATP 7.66129
27 4BKS X6C 8.02469
28 2FB3 GTP 10
29 2DTJ THR 10.1124
30 4FHD EEM 11.413
31 4FHD 0TT 11.413
32 1EWJ BLM 11.9048
33 1W2D 4IP 14.3396
34 1L0I PSR 21.7949
Pocket No.: 2; Query (leader) PDB : 1NJJ; Ligand: ORX; Similar sites found with APoc: 109
This union binding pocket(no: 2) in the query (biounit: 1njj.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 2ZUX RAM 1.41176
2 4CNK MEU 1.53453
3 2RJH DCS 1.84697
4 5GWE GWM 1.97531
5 2YPI PGA 2.02429
6 3RG9 WRA 2.08333
7 3RG9 NDP 2.08333
8 2BL9 NDP 2.10084
9 2BL9 CP6 2.10084
10 1D8C GLV 2.11765
11 4XH0 ADP 2.23325
12 2VAR KDG 2.23642
13 2VAR KDF 2.23642
14 2X1E X1E 2.2409
15 3GD8 GOL 2.24215
16 5YJS SAL 2.30769
17 5FAG PPI 2.43902
18 2CIG 1DG 2.51572
19 2VOH CIT 2.54777
20 2F6U CIT 2.5641
21 5EW9 5VC 2.58303
22 1DNP MHF 2.58824
23 1VFS DCS 2.59067
24 3EEL 53T 2.64317
25 4DE3 DN8 2.6616
26 3EXS 5RP 2.71493
27 1FDJ 13P 2.75482
28 1TRD PGH 2.8
29 6H45 QEI 2.80612
30 2VD9 EPC 2.8133
31 2VD9 IN5 2.8133
32 1ON3 DXX 2.82353
33 4V15 PLP 2.90237
34 3KVY R2B 2.91262
35 1DBT U5P 2.92887
36 6GVZ CHO 2.95082
37 3TAO PGH 2.99625
38 3B0P FMN 3.14286
39 3C3N FMN 3.20513
40 3WXL ADP 3.29412
41 1OLT SAM 3.29412
42 4M3P HCS 3.44828
43 6CUZ FEV 3.60825
44 5EYW PGA 3.61446
45 1SW0 PGA 3.62903
46 1LYX PGA 3.62903
47 3UYW TAU 3.73832
48 1GXS BEZ 3.79747
49 5YSQ INS 3.84615
50 1PVN MZP 4
51 1ME8 RVP 4
52 6FLZ MMA 4.16667
53 1V3S ATP 4.31034
54 5A5W GUO 4.34783
55 1WHT BZS 4.57516
56 5JBX MLI 4.5977
57 1TL2 NDG 4.66102
58 4BI7 PGA 4.66926
59 4YMZ 13P 4.78088
60 5XFV FMN 4.79042
61 4NAE 1GP 4.88889
62 3WQD PLP 999 5.12821
63 1OVD ORO 5.14469
64 1OVD FMN 5.14469
65 1NIU DCS 5.15464
66 4I9A NCN 5.20833
67 2X32 OTP 5.58659
68 6BVE PGA 5.71429
69 4JEJ 1GP 5.7377
70 3JQB DX6 5.90278
71 1TZJ A3B 5.91716
72 1QDS PGA 5.9761
73 2CBO TH2 6.08696
74 3GLC R5P 6.1017
75 3OVR 5SP 6.14035
76 2Y88 2ER 6.14754
77 3AIH BMA MAN MAN 6.45161
78 3MJY IJZ 6.93642
79 3MJY FMN 6.93642
80 1RYD GLC 6.97674
81 1C1D PHE 7.04225
82 4Q86 AMP 7.05882
83 3CTL S6P 7.35931
84 5XSJ XYP 7.43243
85 1M5W DXP 7.81893
86 1EP2 ORO 8.36013
87 5CSS G3P 8.40708
88 5IDB BMA 8.4507
89 2FLI DX5 8.63636
90 1Q6O LG6 8.7963
91 4NFE BEN 8.86076
92 1MVQ MMA 8.8983
93 4DP3 MMV 8.94118
94 4DP3 NDP 8.94118
95 5M4Q PRO 10.1176
96 1AXD GGL CYW GLY 10.5263
97 2BTM PGA 10.7143
98 3KIH GDL 11.3402
99 1W8S FBP 13.308
100 1RL4 BL5 13.8298
101 3UWV 2PG 14.5594
102 4LUT DCS 16.1039
103 5TCI MLI 16.3043
104 5AHN IMP 17.7914
105 3CYQ AMU 19.5652
106 1OFS SUC 20.8333
107 3N2O AG2 24.9412
108 3KIF GDL 34.9057
109 1TUF AZ1 35.2941
Pocket No.: 3; Query (leader) PDB : 1NJJ; Ligand: ORX; Similar sites found with APoc: 15
This union binding pocket(no: 3) in the query (biounit: 1njj.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 1BW9 PPY 2.24719
2 1C1X HFA 2.25352
3 4DPL NAP 3.34262
4 6F3G CJN 3.38983
5 3SRV S19 4.33213
6 4BG4 ARG 4.77528
7 1UYY BGC BGC 5.34351
8 2GNB MAN 5.55556
9 4YEF 4CQ 5.61798
10 3JQ8 DX3 5.90278
11 5TVA AMP 6.66667
12 5HV0 AKG 6.91244
13 2X34 UQ8 7.18232
14 5IDB MAN 8.4507
15 1RJW ETF 8.55457
Pocket No.: 4; Query (leader) PDB : 1NJJ; Ligand: GET; Similar sites found with APoc: 110
This union binding pocket(no: 4) in the query (biounit: 1njj.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 3C6K SPD 1.31234
2 3C6K MTA 1.31234
3 4K38 SAM 1.35135
4 4K39 SAM 1.35135
5 4K37 SAM 1.35135
6 2ZRU FMN 1.3587
7 2BJU IH4 1.41176
8 1U1B PAX 1.6129
9 1I1D 16G 1.86335
10 1E7S NAP 1.86916
11 1Q8Y ADP 1.87668
12 6GBC AMP 1.88235
13 5OMY 9YE 2.04604
14 1I1N SAH 2.21239
15 5V22 SAH 2.3569
16 4KBA 1QM 2.41692
17 4FMU 0UM 2.51799
18 5U6C 7YS 2.53968
19 1JG9 GLC 2.58824
20 2IYA ZIO 2.59434
21 4MFL MFK 2.6087
22 4PU5 ANP 2.64901
23 3C1X CKK 2.68097
24 5JZJ AN2 2.6936
25 5IDM ANP 2.7933
26 1SDW IYT 2.86624
27 2O3Z AI7 2.95203
28 1QK3 5GP 3.00429
29 5MW8 ATP 3.05882
30 4B7H NDP 3.05882
31 1TMM APC 3.16456
32 3FWY ADP 3.18471
33 3DLS ADP 3.28358
34 1OLT SAM 3.29412
35 5IM3 DTP 3.29412
36 1OPK P16 3.29412
37 4O1P ANP 3.29412
38 2UZ1 TPP 3.29412
39 2PID YSA 3.37079
40 1JQ3 AAT 3.37838
41 1LSH PLD 3.44828
42 1ATL 0QI 3.46535
43 6FL8 TIY 3.52941
44 6FL8 ADP 3.52941
45 3KJI ADP 3.54331
46 4IRP UDP 3.58566
47 1MEX RAC 3.75587
48 3SUD SUE 3.94089
49 6GL8 F3Q 4.06977
50 1FP6 ADP 4.15225
51 3TAY MN0 4.29448
52 5NBW 8SK 4.5045
53 2CYE COA 4.51128
54 1ION ADP 4.52675
55 5FM0 WAQ 4.61538
56 5VSM 5AD 4.71698
57 5VSM MET 4.71698
58 3CY2 MB9 4.77707
59 5TWJ SAM 4.93827
60 6BQK Z1E 5.02283
61 3T7V SAM 5.14286
62 4Z87 GDP 5.17647
63 5NJI 8Z2 5.2795
64 2I8T GDD 5.38922
65 1VJY 460 5.61056
66 4YRY FAD 5.7971
67 5XVG 8FX 5.80205
68 4WW7 AMP 5.88235
69 2PT9 2MH 6.23053
70 4P25 FUC GAL NAG FUC 6.29139
71 2XEM SSV 6.66667
72 3IGO ANP 6.82353
73 1TQ4 GDP 7.02179
74 2I7C AAT 7.06714
75 3IQE F42 7.06714
76 3IQE H4M 7.06714
77 1U0J ADP 7.11611
78 2PYW ADP 7.38095
79 2XTN GTP 7.69231
80 4AZ3 S35 7.74194
81 5LXT GDP 7.76053
82 5LXT 7AK 7.76053
83 4V03 ADP 7.76471
84 5TT6 ATP 8.12183
85 4N02 FNR 8.12325
86 4Y85 499 8.13253
87 1BZY IMU 8.29493
88 1G3Q ADP 8.43882
89 3BEO UD1 9.33333
90 4XBA GMP 10
91 4XBA 5GP 10
92 3MQ2 SAH 10.0917
93 2O4N TPV 10.101
94 2TPS TPS 10.1322
95 2G86 UMP 10.7595
96 2BKK ADP 10.9848
97 3TM0 B31 11.0266
98 3TM0 ANP 11.0266
99 3EYA TDP 11.0588
100 5G1X ADP 11.1111
101 2O07 MTA 11.1842
102 2O07 SPD 11.1842
103 6AR9 3L4 11.3971
104 3AB4 THR 11.7978
105 3MEH THP 13.2867
106 2DT9 THR 13.7725
107 4Q5H ANP 14.4737
108 3HAV ATP 16.7224
109 2E56 MYR 18.0556
110 3A6T 8OG 22.4806
Pocket No.: 5; Query (leader) PDB : 1NJJ; Ligand: ORX; Similar sites found with APoc: 6
This union binding pocket(no: 5) in the query (biounit: 1njj.bio2) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 5HWV MBN None
2 4JZ8 CIT 1.89274
3 1QVJ RP5 6.84932
4 1BXG HCI 7.02247
5 1X1Z BMP 8.33333
6 3WG3 A2G GAL NAG FUC 17.4157
Pocket No.: 6; Query (leader) PDB : 1NJJ; Ligand: GET; Similar sites found with APoc: 62
This union binding pocket(no: 6) in the query (biounit: 1njj.bio2) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 1QPB TPP 1.41176
2 4BHN BH9 1.49701
3 4NMC FAD 1.64706
4 4CTA ATP 1.77665
5 2HGS ADP 1.88235
6 3RFA SAM 1.9802
7 3NEM AMO 2.11765
8 3AKK ADP 2.15385
9 5TH5 7C5 2.28137
10 3PLS ANP 2.34899
11 4UWJ MYA 2.457
12 4UWJ 7L5 2.457
13 3VPD ANP 2.4911
14 4GYI ADP 2.51889
15 5K2M ADP 2.5641
16 4NJH SAM 2.6087
17 4NJH 2K8 2.6087
18 1OBD ATP 2.61438
19 4XDU ADP 2.64706
20 3FSY SCA 2.71084
21 3OID NDP 2.71318
22 6H3O FAD 2.82353
23 1VG8 GNP 2.89855
24 2PUL ACP 3.02267
25 1WVG CXY 3.06407
26 5W8Q BU4 3.07692
27 1T36 ADP 3.14136
28 2PZI AXX 3.29412
29 4BS0 6NT 3.45912
30 3UDZ ADP 3.52941
31 2RIF AMP 3.5461
32 5C1P ADP 3.59477
33 3P3G UKW 3.66667
34 3P3G 3P3 3.66667
35 5A3T MMK 3.76471
36 2R40 EPH 3.80228
37 3VPC ADP 3.90071
38 4CRL C1I 3.94089
39 4LRJ ANP 4.14201
40 3TII ANP 4.21053
41 2ZAT NAP 4.23077
42 2V58 LZJ 4.70588
43 3F5O UOC COA 4.72973
44 4Y0X ADP 4.8
45 4M20 COA 5.51181
46 3V1U NAD 5.62771
47 2GU8 796 5.93472
48 1PK8 ATP 6.16114
49 3X01 AMP 6.87023
50 5EH0 5NW 7.75194
51 5LXT ACP 7.76053
52 2JLB UDM 7.76471
53 2AQX ATP 7.95848
54 5TBM 79A 8.54701
55 4F9C 0SX 9.02778
56 5ZCT ANP 9.15033
57 2FB3 5AD 10
58 2FB3 MET 10
59 4GO7 THR 10.5
60 6G9I CXX 12.5
61 3MWS 017 17.1717
62 2HKA C3S 31.5385
Pocket No.: 7; Query (leader) PDB : 1NJJ; Ligand: ORX; Similar sites found with APoc: 5
This union binding pocket(no: 7) in the query (biounit: 1njj.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 3G6M CFF 1.72414
2 2RDE C2E 3.58566
3 4CUB GAL NAG 4.91803
4 5EEH P9P 5.41176
5 4AF5 CIT 8.42105
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