Receptor
PDB id Resolution Class Description Source Keywords
1F3T 2 Å EC: 4.1.1.17 CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYL COMPLEXED WITH PUTRESCINE, ODC'S REACTION PRODUCT. TRYPANOSOMA BRUCEI BETA-ALPHA-BARREL MODIFIED GREEK KEY BETA-SHEET LYASE
Ref.: ALTERING THE REACTION SPECIFICITY OF EUKARYOTIC ORN DECARBOXYLASE. BIOCHEMISTRY V. 39 11247 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PLP PUT A:1001;
B:1003;
C:1005;
D:1007;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
316.274 n/a [P+](...
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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 DECARBOXYLASE BOUND TO D-ORNITHINE AND TO G418 TRYPANOSOMA BRUCEI GAMBIENSE ORNITHINE DECARBOXYLASE ODC PLP PYRIDOXAL 5-prime -PHOSPHATE D-ORNITHINE G418 LYASE
Ref.: X-RAY STRUCTURE DETERMINATION OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE BOUND TO D-ORNITHINE AND TO G418: INSIGHTS INTO SUBSTRATE BINDING AND ODC CONFORMATIONAL 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: PLP PUT; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP PUT 1 1
2 PLP ABU 0.742857 0.907407
3 P3D 0.638889 0.830508
4 LLP 0.5875 0.803279
5 EXT 0.569444 0.839286
6 Z98 0.525 0.758065
7 0JO 0.513158 0.721311
8 PLP MYB 0.494382 0.753846
9 4LM 0.493506 0.704918
10 EPC 0.493333 0.767857
11 PLP PHE 0.488636 0.836364
12 PLP PVH 0.467391 0.69697
13 P89 0.465909 0.75
14 PLP 0.463768 0.684211
15 PLP 142 0.463158 0.69697
16 KOU 0.4625 0.75
17 6DF 0.457831 0.754386
18 PZP 0.457143 0.75
19 MPM 0.45 0.758621
20 PL5 0.443182 0.754098
21 PL6 0.440476 0.762712
22 HCP 0.439024 0.810345
23 5DK 0.428571 0.761905
24 PLP PMP 0.4125 0.75
25 FOO 0.4125 0.7
26 PUS 0.411111 0.642857
27 AN7 0.4 0.661017
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1NJJ; Ligand: GET; Similar sites found: 11
This union binding pocket(no: 1) in the query (biounit: 1njj.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5CDH TLA 0.02605 0.40248 2.67857
2 2DBZ NAP 0.02266 0.40787 3.89222
3 3ZW2 GAL FUC 0.007219 0.41026 4.5977
4 3ZW2 NAG GAL FUC 0.008793 0.40848 4.5977
5 3A5Z KAA 0.0187 0.4121 5.75916
6 4D4U FUC NDG GAL FUC 0.01636 0.40207 7.61905
7 2FB3 GTP 0.01426 0.41806 10
8 4FHD 0TT 0.006846 0.43674 11.413
9 4FHD EEM 0.006846 0.43674 11.413
10 1EWJ BLM 0.01847 0.41481 11.9048
11 1L0I PSR 0.004087 0.4341 21.7949
Pocket No.: 2; Query (leader) PDB : 1NJJ; Ligand: ORX; Similar sites found: 49
This union binding pocket(no: 2) in the query (biounit: 1njj.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5GWE GWM 0.02432 0.40036 1.97531
2 2YPI PGA 0.001499 0.45566 2.02429
3 3RG9 WRA 0.01387 0.4052 2.08333
4 3RG9 NDP 0.0143 0.40154 2.08333
5 2BL9 CP6 0.01352 0.40368 2.10084
6 1D8C GLV 0.003586 0.4222 2.11765
7 4XH0 ADP 0.03104 0.40056 2.23325
8 5FAG PPI 0.009882 0.40057 2.43902
9 2CIG 1DG 0.01991 0.40178 2.51572
10 2VOH CIT 0.03429 0.407 2.54777
11 2F6U CIT 0.01222 0.41998 2.5641
12 3EXS 5RP 0.003402 0.43831 2.71493
13 2VD9 IN5 0.01084 0.40221 2.8133
14 4V15 PLP 0.0006206 0.4688 2.90237
15 1DBT U5P 0.003399 0.41746 2.92887
16 3TAO PGH 0.001098 0.40011 2.99625
17 3B0P FMN 0.00646 0.41246 3.14286
18 5EYW PGA 0.001524 0.46071 3.61446
19 1SW0 PGA 0.002198 0.44269 3.62903
20 1GXS BEZ 0.02597 0.40377 3.79747
21 1ME8 RVP 0.01032 0.40891 4
22 1V3S ATP 0.002569 0.41099 4.31034
23 5A5W GUO 0.00815 0.41659 4.34783
24 1WHT BZS 0.02377 0.4035 4.57516
25 4YMZ 13P 0.00126 0.46482 4.78088
26 4NAE 1GP 0.0052 0.43825 4.88889
27 3WQD PLP 999 0.004804 0.41452 5.12821
28 2SFP PPI 0.01147 0.40109 5.15464
29 4I9A NCN 0.007181 0.40675 5.20833
30 2X32 OTP 0.02301 0.40058 5.58659
31 2CBO TH2 0.01131 0.41987 6.08696
32 3GLC R5P 0.003914 0.43076 6.1017
33 3OVR 5SP 0.001569 0.42635 6.14035
34 2Y88 2ER 0.004961 0.42198 6.14754
35 3AIH BMA MAN MAN 0.02708 0.40159 6.45161
36 3MJY IJZ 0.01273 0.40042 6.93642
37 3MJY FMN 0.01273 0.40042 6.93642
38 1RYD GLC 0.00666 0.43756 6.97674
39 4Q86 AMP 0.01232 0.40701 7.05882
40 3CTL S6P 0.004723 0.40078 7.35931
41 1M5W DXP 0.01564 0.41445 7.81893
42 5CSS G3P 0.003381 0.4434 8.40708
43 2FLI DX5 0.001905 0.42097 8.63636
44 1Q6O LG6 0.001147 0.41411 8.7963
45 1AXD GGL CYW GLY 0.02848 0.40228 10.5263
46 1RL4 BL5 0.0145 0.41962 13.8298
47 5TCI MLI 0.005149 0.44266 16.3043
48 3CYQ AMU 0.01563 0.4179 19.5652
49 1TUF AZ1 0.000000003712 0.61864 35.2941
Pocket No.: 3; Query (leader) PDB : 1NJJ; Ligand: ORX; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1njj.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1NJJ; Ligand: GET; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1njj.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1NJJ; Ligand: ORX; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 1njj.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1NJJ; Ligand: GET; Similar sites found: 41
This union binding pocket(no: 6) in the query (biounit: 1njj.bio2) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4K38 SAM 0.0109 0.42628 1.35135
2 4K39 SAM 0.0128 0.42199 1.35135
3 4CTA ATP 0.03011 0.40455 1.77665
4 2HGS ADP 0.01049 0.42746 1.88235
5 3RFA SAM 0.006079 0.435 1.9802
6 3AKK ADP 0.02858 0.40282 2.15385
7 3PLS ANP 0.02096 0.40941 2.34899
8 3VPD ANP 0.01066 0.42847 2.4911
9 5K2M ADP 0.009114 0.43509 2.5641
10 2IYA ZIO 0.03242 0.40575 2.59434
11 1OBD ATP 0.01535 0.40943 2.61438
12 1VG8 GNP 0.03466 0.40538 2.89855
13 5MW8 ATP 0.007726 0.43652 3.05882
14 1WVG CXY 0.01581 0.41839 3.06407
15 1T36 ADP 0.01987 0.41932 3.14136
16 3DLS ADP 0.02268 0.40271 3.28358
17 4BS0 6NT 0.005017 0.42992 3.45912
18 3UDZ ADP 0.01541 0.41454 3.52941
19 3P3G 3P3 0.03325 0.40692 3.66667
20 3P3G UKW 0.03325 0.40692 3.66667
21 5A3T MMK 0.02436 0.41533 3.76471
22 3SUD SUE 0.01877 0.41258 3.94089
23 4LRJ ANP 0.02151 0.40192 4.14201
24 3TII ANP 0.0149 0.40973 4.21053
25 3F5O UOC COA 0.03315 0.40499 4.72973
26 4Y0X ADP 0.01746 0.40615 4.8
27 4M20 COA 0.02109 0.41323 5.51181
28 3V1U NAD 0.02319 0.41072 5.62771
29 4WW7 AMP 0.01988 0.40996 5.88235
30 4R33 SAH 0.0375 0.40898 6.66667
31 4R33 TRP 0.0375 0.40898 6.66667
32 2JLB UDM 0.03843 0.40298 7.76471
33 2AQX ATP 0.006787 0.43915 7.95848
34 4F9C 0SX 0.02035 0.41053 9.02778
35 2FB3 5AD 0.008956 0.42378 10
36 2FB3 MET 0.008482 0.423 10
37 4GO7 THR 0.01973 0.40356 10.5
38 2BKK ADP 0.01657 0.40761 10.9848
39 3KA2 2NC 0.009993 0.4555 11.33
40 2DT9 THR 0.007599 0.41237 13.7725
41 2E56 MYR 0.03811 0.40778 18.0556
Pocket No.: 7; Query (leader) PDB : 1NJJ; Ligand: ORX; Similar sites found: 4
This union binding pocket(no: 7) in the query (biounit: 1njj.bio2) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3G6M CFF 0.01475 0.41521 1.72414
2 4CUB GAL NAG 0.02878 0.40086 4.91803
3 5TVA AMP 0.01665 0.40459 6.66667
4 4DP3 MMV 0.02147 0.40197 8.94118
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