-->
Receptor
PDB id Resolution Class Description Source Keywords
2NVA 1.8 Å EC: 4.1.1.19 THE X-RAY CRYSTAL STRUCTURE OF THE PARAMECIUM BURSARIA CHLOR ARGININE DECARBOXYLASE BOUND TO AGMATINE PARAMECIUM BURSARIA CHLORELLA VIRUS 1 ARGININE DECARBOXYLASE PLP TIM BARREL EUKARYOTIC ODC-LIKE
Ref.: X-RAY STRUCTURE OF PARAMECIUM BURSARIA CHLORELLA VI ARGININE DECARBOXYLASE: INSIGHT INTO THE STRUCTURAL FOR SUBSTRATE SPECIFICITY. BIOCHEMISTRY V. 46 2831 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PL2 A:2001;
B:2002;
C:2003;
D:2004;
E:2005;
F:2006;
G:2007;
H:2008;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
361.334 C13 H24 N5 O5 P [H]/N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2NVA 1.8 Å EC: 4.1.1.19 THE X-RAY CRYSTAL STRUCTURE OF THE PARAMECIUM BURSARIA CHLOR ARGININE DECARBOXYLASE BOUND TO AGMATINE PARAMECIUM BURSARIA CHLORELLA VIRUS 1 ARGININE DECARBOXYLASE PLP TIM BARREL EUKARYOTIC ODC-LIKE
Ref.: X-RAY STRUCTURE OF PARAMECIUM BURSARIA CHLORELLA VI ARGININE DECARBOXYLASE: INSIGHT INTO THE STRUCTURAL FOR SUBSTRATE SPECIFICITY. BIOCHEMISTRY V. 46 2831 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 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....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 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....
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: PL2; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 PL2 1 1
2 PLG 0.611111 0.794118
3 33P 0.558442 0.791045
4 P1T 0.545455 0.760563
5 EA5 0.542169 0.84058
6 IN5 0.526316 0.776119
7 PDA 0.525641 0.753623
8 PP3 0.525641 0.753623
9 PDD 0.525641 0.753623
10 IK2 0.518987 0.760563
11 QLP 0.518072 0.802817
12 PE1 0.517647 0.865672
13 PMP 0.514286 0.84127
14 PLS 0.5125 0.794118
15 2BO 0.5125 0.753623
16 2BK 0.5125 0.753623
17 5PA 0.5125 0.785714
18 TLP 0.5125 0.753623
19 HEY 0.511905 0.774648
20 C6P 0.506173 0.794118
21 PPD 0.506173 0.794118
22 ILP 0.506024 0.757143
23 ORX 0.505882 0.865672
24 PLA 0.5 0.75
25 PY5 0.5 0.8
26 PXP 0.5 0.75
27 LPI 0.5 0.791667
28 PY6 0.494118 0.802817
29 PMH 0.493827 0.65
30 PL4 0.488636 0.865672
31 N5F 0.488372 0.838235
32 PSZ 0.488372 0.693333
33 3LM 0.488372 0.72973
34 7XF 0.488095 0.823529
35 PDG 0.488095 0.823529
36 CBA 0.488095 0.722222
37 PGU 0.488095 0.823529
38 GT1 0.486111 0.701493
39 PMG 0.482353 0.777778
40 76U 0.476744 0.811594
41 7TS 0.470588 0.619048
42 PL8 0.466667 0.727273
43 9YM 0.465909 0.797101
44 DCS 0.465116 0.666667
45 KAM 0.461538 0.811594
46 7B9 0.456522 0.756757
47 RW2 0.455556 0.763889
48 PXG 0.455556 0.742857
49 EQJ 0.445652 0.878788
50 5DK 0.445652 0.878788
51 AQ3 0.427083 0.75
52 PPG 0.419355 0.838235
53 PLP 2KZ 0.418605 0.714286
54 DOW 0.407407 0.767123
55 PLR 0.402778 0.661538
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2NVA; Ligand: PL2; Similar sites found with APoc: 151
This union binding pocket(no: 1) in the query (biounit: 2nva.bio2) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 4YMZ 13P 1.19522
2 3LJU IP9 1.34409
3 1FDJ 13P 1.37741
4 1FDJ 2FP 1.37741
5 5VLC HSO 1.6129
6 3WQD PLP 999 1.6129
7 5O9W AKG 1.63488
8 6CZY PMP 1.65746
9 3WBZ ATP 1.84502
10 2JK0 ASP 1.84615
11 2RJH DCS 1.88172
12 5FWJ MMK 1.88172
13 3PNQ 2HA 1.96078
14 2YGM GLA NAG GAL FUC 1.9774
15 2RDE C2E 1.99203
16 2VDJ HSE 1.99336
17 4I9A NCN 2.08333
18 3TUR DGL 2.09059
19 4V15 PLP 2.15054
20 3TKY N7I 2.17391
21 5CPR 539 2.23881
22 4BI7 PGA 2.33463
23 1VFS DCS 2.41935
24 6GW4 CHO 2.60586
25 1F76 ORO 2.67857
26 5JBX MLI 2.68199
27 4AF0 MOA 2.68817
28 5GOP FRU 2.68817
29 3GLC R5P 2.71186
30 5A5W GUO 2.7668
31 2AKO ADP 2.78884
32 5IDB BMA 2.8169
33 5IDB MAN 2.8169
34 1YQT ADP 2.95699
35 1YFS ALA 2.95699
36 1CX9 NHP 2.98507
37 2F6U CIT 2.99145
38 1V6A TRE 3.01205
39 2AZ3 CDP 3.04878
40 2X61 CH 3.10078
41 5YSQ INS 3.14685
42 2Y88 2ER 3.27869
43 1FQK ALF 3.38462
44 3ROE THM 3.39623
45 6F9G PUT 3.42679
46 4D52 GIV 3.49206
47 4D52 GXL 3.49206
48 6DND PLP 3.49462
49 6FYV 3NG 3.56083
50 4WAS COO 3.57143
51 1QDS PGA 3.58566
52 1PU7 39A 3.66972
53 1M5W DXP 3.7037
54 6F3G CJN 3.72881
55 5AHN IMP 3.88548
56 2BTM PGA 3.96825
57 5EY0 GTP 4.0146
58 5EYW PGA 4.01606
59 2OVR SER LEU ILE PRO TPO PRO ASP LYS 4.02685
60 1LYX PGA 4.03226
61 5YV5 ADP 4.03226
62 4JEJ 1GP 4.09836
63 5AYE BMA BMA 4.1791
64 1W8S FBP 4.18251
65 5TVF PUT 4.21053
66 5TVM PUT 4.21053
67 4NFE BEN 4.21941
68 5EEH P9P 4.25532
69 6GVZ CHO 4.2623
70 4UTU LRY 4.36681
71 4UTW RFW 4.36681
72 2VNO GAL GAL FUC 4.44444
73 4NV1 TYD 4.52675
74 3N9R TD3 4.56026
75 5WAN URA 4.56989
76 5YJS SAL 4.56989
77 1OKE BOG 4.56989
78 1KC7 PPR 4.56989
79 1DBT U5P 4.60251
80 5Y02 MXN 4.6729
81 1SQL GUN 4.79452
82 4I4S LAT 4.79452
83 1SW0 PGA 4.83871
84 4FFG LBS 4.83871
85 6HLY G9Z 4.83871
86 3AIH BMA MAN MAN 4.83871
87 6BVE PGA 4.89796
88 1BXG HCI 5.05618
89 1BW9 PPY 5.05618
90 1C1X HFA 5.07042
91 1C1D PHE 5.07042
92 1TL2 NDG 5.08475
93 2PYW SR1 5.10753
94 4LUT DCS 5.10753
95 3LL5 IP8 5.22088
96 5YW0 SIN 5.34591
97 1ON3 DXX 5.37634
98 5GMH RX8 5.37634
99 5HWV MBN 5.38462
100 6FLZ MMA 5.55556
101 2BS5 BGC GAL FUC 5.55556
102 3TAO PGH 5.64516
103 5EJL C2E 5.64516
104 4G7A AZM 5.64516
105 2YPI PGA 5.66802
106 3UWV 2PG 5.74713
107 3EXS 5RP 5.88235
108 1SLT NDG GAL 5.97015
109 1NXJ TLA 6.01093
110 4HDK 13X 6.03448
111 3N29 NSD 6.1828
112 4CNK MEU 6.1828
113 1U6R ADP 6.45161
114 1NIU DCS 6.45161
115 3B0P FMN 6.57143
116 5CSS G3P 6.63717
117 2OEM 1AE 6.72043
118 2VD9 EPC 6.72043
119 2VD9 IN5 6.72043
120 2R2N PMP 6.72043
121 3EB9 FLC 6.76692
122 1TRD PGH 6.8
123 5O6Y 5YA 7.00935
124 4YLZ LAT NAG GAL 7.18954
125 3CTL S6P 7.35931
126 3OVR 5SP 7.45614
127 3SAO NKN 7.5
128 1UYY BGC BGC 7.63359
129 4NAE 1GP 8
130 3W9Z FMN 8.07453
131 4FHT DHB 8.28025
132 5TCI MLI 8.33333
133 5YRL GLC GLC 8.4507
134 1KNM LAT 8.46154
135 4UMJ BFQ 8.78378
136 1XVB BBU 8.82353
137 4TR9 ASP TRP ASN 8.94309
138 2FLI DX5 9.09091
139 1Q6O LG6 9.72222
140 3KVY R2B 10.356
141 4CPA GLY 10.5263
142 2YVE MBT 10.8108
143 5Y4R C2E 11.0345
144 5KAX RHQ 11.4458
145 4EWN 0VR 13.0435
146 3KIF GDL 16.0377
147 2C49 ADN 18.543
148 1YRO UDP 23.5772
149 1TUF AZ1 34.4086
150 5GJO PLP 45.4301
151 2PLK P3D 45.6989
Pocket No.: 2; Query (leader) PDB : 2NVA; Ligand: PL2; Similar sites found with APoc: 29
This union binding pocket(no: 2) in the query (biounit: 2nva.bio2) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 2IF8 ADP 1.92837
2 3HYW DCQ 2.15054
3 5J75 6GQ 2.27273
4 3BF1 PAU 2.81124
5 3O5X JZG 2.89855
6 2F9W PAU 2.95203
7 2X5D PLP 3.22581
8 5T7I LAT NAG GAL 3.22581
9 2IMP LAC 3.49462
10 4R5Z PMP 3.54223
11 1U29 I3P 3.87597
12 1V2F HCI 4.03226
13 2EG5 XTS 4.30108
14 3BRN SRO 4.4586
15 5A1S FLC 4.56989
16 5FS0 5JC 5.21327
17 1A78 TDG 5.22388
18 3BKR PLM 5.55556
19 1GXS DKA 5.92593
20 3AXM 6PG 6.20155
21 3CQ5 PMP 7.04607
22 1UJ5 5RP 7.92952
23 4KAX 4IP 9.46746
24 1OFZ FUL 9.9359
25 6BVM EBV 11.976
26 3ZXE PGZ 15.0376
27 4D06 NAR 15.1943
28 1UPF URF 18.75
29 1KO0 DLY 37.9032
Pocket No.: 3; Query (leader) PDB : 2NVA; Ligand: PL2; Similar sites found with APoc: 21
This union binding pocket(no: 3) in the query (biounit: 2nva.bio4) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 5XPI 8C3 1.91083
2 1TW4 CHD 2.4
3 5GOO FRU 2.68817
4 1NVM OXL 2.88462
5 5M4Q PRO 2.95699
6 5X80 SAL 3.125
7 1H16 PYR 3.22581
8 1DMH MCT 3.53698
9 2Y7P SAL 3.66972
10 4M26 AKG 3.84615
11 3L6C MLI 4.03226
12 2YAJ 4HP 5.10753
13 3SRV S19 5.41516
14 1GXS BEZ 5.92593
15 3KIH GDL 6.18557
16 1WQ1 AF3 8.43373
17 1WW5 SGA BGC 8.75
18 2CJU PHX 9.09091
19 4RJD TFP 9.09091
20 6BVK EAV 11.976
21 4KBB BGC GAL SIA NGA GAL SIA 20.5882
Pocket No.: 4; Query (leader) PDB : 2NVA; Ligand: PL2; Similar sites found with APoc: 16
This union binding pocket(no: 4) in the query (biounit: 2nva.bio4) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 5KF6 TFB 2.15054
2 4M3P HCS 2.15054
3 1TZD ADP 2.18182
4 5TED SKM 2.21239
5 3RGA LSB 2.4735
6 3R7F CP 2.63158
7 4CCW VKC 3.67893
8 4MBY BGC SIA GAL 3.95683
9 1DQX BMP 4.11985
10 1JE1 GMP 5.50847
11 1QH8 HCA 5.64516
12 1GXU 2HP 6.59341
13 1FHW I5P 6.97674
14 4JZ8 CIT 8.83281
15 5AHM IMP 12.0968
16 2AK5 ARG PRO PRO LYS PRO ARG PRO ARG 12.5
Pocket No.: 5; Query (leader) PDB : 2NVA; Ligand: PL2; Similar sites found with APoc: 13
This union binding pocket(no: 5) in the query (biounit: 2nva.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 5G3R 89A 2.55682
2 2XAU ADP 2.68817
3 5NC9 8SZ 2.83401
4 4BHL ARG 3.65169
5 3A16 PXO 3.76344
6 5HV0 AKG 4.14747
7 5GVR LMR 4.2735
8 5HUA FK5 6.95652
9 5CIC 51R 9.25926
10 5C3R AKG 9.62099
11 5C3R HMU 9.62099
12 5EPQ OLA 11.5854
13 5XDR ADP 14.2473
Pocket No.: 6; Query (leader) PDB : 2NVA; Ligand: PL2; Similar sites found with APoc: 13
This union binding pocket(no: 6) in the query (biounit: 2nva.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 2DPY ADP 2.15054
2 1DKU AP2 2.2082
3 1W6P NDG GAL 3.73134
4 4TVD BGC 4.03226
5 6B9R 2HE 4.30108
6 4YMJ 4EJ 4.60526
7 3PD6 PMP 5.10753
8 5OFI 9TQ 5.7377
9 6B9T 2HE 6.1828
10 1OW4 2AN 6.20155
11 2A19 ANP 8.57143
12 1K7U NAG NAG 9.67742
13 5C2N NAG 22.9167
Pocket No.: 7; Query (leader) PDB : 2NVA; Ligand: PL2; Similar sites found with APoc: 4
This union binding pocket(no: 7) in the query (biounit: 2nva.bio3) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 4JAW GAL NGT 2.41935
2 3HSS MLA 3.07167
3 3HAV ATP 10.0334
4 5ME4 HP4 11.3139
Pocket No.: 8; Query (leader) PDB : 2NVA; Ligand: PL2; Similar sites found with APoc: 4
This union binding pocket(no: 8) in the query (biounit: 2nva.bio3) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 1YQZ FAD 4.10959
2 6AYU MLI 5.18732
3 2Z77 NCA 7.19424
4 5KEW 6SB 20.8333
APoc FAQ
Feedback