Receptor
PDB id Resolution Class Description Source Keywords
5Z2L 1.7 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF BDCA IN COMPLEX WITH NADPH ESCHERICHIA COLI (STRAIN K12) SHORT-CHAIN DEHYDROGENASE/REDUCTASE (SDR) NADPH BINDING BIDISPERSAL OXIDOREDUCTASE
Ref.: A POTENTIAL SUBSTRATE BINDING POCKET OF BDCA PLAYS CRITICAL ROLE IN NADPH RECOGNITION AND BIOFILM DISP BIOCHEM. BIOPHYS. RES. V. 497 863 2018 COMMUN.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO G:301;
B:301;
C:303;
E:302;
I:301;
C:302;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
PEG K:301;
Invalid;
none;
submit data
106.12 C4 H10 O3 C(COC...
NDP J:301;
A:302;
L:301;
F:302;
G:302;
C:304;
I:302;
K:302;
D:301;
E:303;
B:302;
H:301;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
Kd = 45 uM
745.421 C21 H30 N7 O17 P3 c1nc(...
PG0 A:301;
Invalid;
none;
submit data
120.147 C5 H12 O3 COCCO...
GOL C:301;
E:301;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
PG4 F:301;
Invalid;
none;
submit data
194.226 C8 H18 O5 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5Z2L 1.7 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF BDCA IN COMPLEX WITH NADPH ESCHERICHIA COLI (STRAIN K12) SHORT-CHAIN DEHYDROGENASE/REDUCTASE (SDR) NADPH BINDING BIDISPERSAL OXIDOREDUCTASE
Ref.: A POTENTIAL SUBSTRATE BINDING POCKET OF BDCA PLAYS CRITICAL ROLE IN NADPH RECOGNITION AND BIOFILM DISP BIOCHEM. BIOPHYS. RES. V. 497 863 2018 COMMUN.
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 510 families.
1 5Z2L Kd = 45 uM NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 391 families.
1 5Z2L Kd = 45 uM NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
50% Homology Family (47)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2VZ0 Ki = 9.8 nM D64 C15 H14 N4 Cc1ccc(cc1....
2 1VL8 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
3 1X7G - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
4 2RH4 Ki = 15 uM EMO C15 H10 O5 Cc1cc2c(c(....
5 4N5M - CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
6 4BNV ic50 = 0.03 uM Q7U C15 H13 Cl N4 O Cn1c2ccccc....
7 4BO1 ic50 = 0.05 uM NKH C18 H15 Cl N2 O3 COc1cc(c(c....
8 4BO0 ic50 = 0.2 uM FXE C17 H18 N4 O3 Cn1c2cccc(....
9 1H5Q - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
10 2AE2 - PTO C8 H15 N O CN1[C@H]2C....
11 1NFF - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
12 1XKQ - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
13 5YSS - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
14 3SJ7 Kd = 53.93 uM NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
15 1ZEM - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
16 5O43 Ki = 42 nM 9JQ C18 H14 F2 N2 O2 CN(c1ccc(c....
17 5EN4 Ki = 64 nM 5Q6 C18 H12 F N O4 c1cc(c(c(c....
18 5O6X Ki = 6 nM 9MK C17 H12 F N O2 Cc1ccc2c(c....
19 5L7T Ki = 26 nM 6QJ C19 H14 F N O3 Cc1cc(ccc1....
20 1ZJZ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
21 1ZJY - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
22 2WDZ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
23 2Q2V - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
24 3NUG - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
25 1G0O Ki = 14 nM PYQ C11 H11 N O c1cc2c3c(c....
26 4GH5 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
27 1RWB - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
28 5Z2L Kd = 45 uM NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
29 5T2U - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
30 4NBU - CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
31 4KWH - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
32 4KWI - 1TJ C19 H12 O5 Cc1cc2c(c(....
33 5OJG - BUO C4 H6 O2 CC(=O)C(=O....
34 2CFC - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
35 3ICC - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
36 3AI3 - SOE C6 H12 O6 C1[C@@H]([....
37 1AHI - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
38 5B4T - 3HR C4 H8 O3 C[C@H](CC(....
39 3VDQ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
40 2DTX - BMA C6 H12 O6 C([C@@H]1[....
41 2DTE - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
42 2AG5 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
43 1JA9 Ki = 420 nM PYQ C11 H11 N O c1cc2c3c(c....
44 1UZN Kd = 11.2 uM NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
45 3QWF - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
46 3AFN - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
47 1XHL - TNE C8 H13 N O CN1[C@H]2C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NDP; Similar ligands found: 172
No: Ligand ECFP6 Tc MDL keys Tc
1 NDP 1 1
2 0WD 0.827273 1
3 NAI 0.803738 0.986842
4 NMN AMP PO4 0.794643 0.948052
5 NPW 0.692308 0.962025
6 NZQ 0.686441 0.987013
7 1DG 0.68 1
8 DG1 0.68 1
9 A2R 0.650943 0.909091
10 A22 0.64486 0.934211
11 TXP 0.644628 0.924051
12 ATR 0.640777 0.894737
13 NA7 0.636364 0.886076
14 XNP 0.620968 0.949367
15 AP0 0.598361 0.948718
16 A2P 0.598039 0.881579
17 NJP 0.574803 0.923077
18 25L 0.550847 0.934211
19 ODP 0.550388 0.936709
20 NAX 0.544 0.949367
21 25A 0.53913 0.921053
22 80F 0.537879 0.914634
23 2AM 0.529412 0.87013
24 6V0 0.519685 0.974026
25 NAP 0.514493 0.922078
26 7L1 0.507143 0.763441
27 EAD 0.507143 0.949367
28 A2D 0.504673 0.921053
29 TXE 0.503876 0.935897
30 NA0 0.496454 0.910256
31 TXD 0.496124 0.911392
32 SAP 0.495575 0.875
33 AGS 0.495575 0.875
34 P1H 0.493056 0.925926
35 CO7 0.489796 0.791209
36 TAP 0.489362 0.864198
37 PAP 0.482456 0.907895
38 BA3 0.481818 0.921053
39 NAJ PZO 0.478261 0.924051
40 ATP 0.477876 0.921053
41 HEJ 0.477876 0.921053
42 B4P 0.477477 0.921053
43 AP5 0.477477 0.921053
44 ADP 0.477477 0.921053
45 OAD 0.47541 0.897436
46 AR6 0.473684 0.896104
47 AQP 0.473684 0.921053
48 5FA 0.473684 0.921053
49 APR 0.473684 0.896104
50 AN2 0.473214 0.909091
51 3OD 0.467742 0.897436
52 50T 0.464912 0.884615
53 NAJ PYZ 0.464789 0.879518
54 9X8 0.463415 0.851852
55 PO4 PO4 A A A A PO4 0.463415 0.857143
56 V3L 0.461538 0.896104
57 2A5 0.46087 0.85
58 AT4 0.460177 0.886076
59 A1R 0.459016 0.841463
60 4AD 0.459016 0.875
61 ADQ 0.459016 0.897436
62 OVE 0.458716 0.8375
63 OMR 0.458647 0.813953
64 PPS 0.457627 0.811765
65 AD9 0.456897 0.897436
66 CA0 0.45614 0.897436
67 M33 0.45614 0.884615
68 ADJ 0.455882 0.879518
69 A3P 0.455357 0.894737
70 ACP 0.452174 0.897436
71 ENP 0.451613 0.85
72 UP5 0.451128 0.948052
73 SRP 0.45 0.8625
74 ANP 0.449153 0.897436
75 ACQ 0.449153 0.897436
76 PRX 0.448276 0.82716
77 A3R 0.447154 0.841463
78 5AL 0.445378 0.884615
79 7D4 0.443478 0.8375
80 ADX 0.443478 0.811765
81 6YZ 0.438017 0.897436
82 A 0.436364 0.894737
83 AMP 0.436364 0.894737
84 4TC 0.433824 0.924051
85 7D3 0.433628 0.8375
86 DCA 0.433566 0.788889
87 ETB 0.433566 0.797753
88 BIS 0.433071 0.864198
89 1ZZ 0.433071 0.802326
90 00A 0.432 0.864198
91 ATF 0.429752 0.886076
92 DQV 0.428571 0.934211
93 0T1 0.427586 0.788889
94 5SV 0.427419 0.788235
95 8QN 0.427419 0.884615
96 3AM 0.427273 0.857143
97 N01 0.426573 0.884615
98 PR8 0.425197 0.811765
99 LAD 0.425197 0.821429
100 WAQ 0.425197 0.841463
101 DTP 0.425 0.8375
102 AMO 0.424 0.886076
103 PAJ 0.424 0.843373
104 APC 0.423729 0.886076
105 UPA 0.423358 0.935897
106 48N 0.422222 0.853659
107 FYA 0.421875 0.860759
108 PTJ 0.421875 0.853659
109 CNA 0.421429 0.910256
110 PUA 0.42069 0.9125
111 DND 0.419118 0.910256
112 NXX 0.419118 0.910256
113 AV2 0.418033 0.848101
114 COA 0.417808 0.788889
115 3UK 0.417323 0.897436
116 OOB 0.416 0.909091
117 IVC 0.415584 0.78022
118 DAT 0.415254 0.8375
119 NDO 0.414966 0.897436
120 139 0.414286 0.901235
121 B5V 0.414062 0.886076
122 T99 0.413223 0.886076
123 TAT 0.413223 0.886076
124 3AT 0.413223 0.896104
125 YLB 0.413043 0.784091
126 62F 0.4125 0.823529
127 ABM 0.412281 0.848101
128 B5M 0.412214 0.875
129 YAP 0.412214 0.875
130 YLP 0.411765 0.784091
131 NB8 0.410853 0.853659
132 ME8 0.410853 0.802326
133 SON 0.410256 0.886076
134 DLL 0.409449 0.909091
135 AHX 0.409449 0.853659
136 CAO 0.409396 0.763441
137 30N 0.409396 0.72449
138 AMX 0.409396 0.797753
139 COS 0.409396 0.771739
140 7D5 0.409091 0.8125
141 4UW 0.408759 0.9125
142 F2R 0.408451 0.825581
143 APX 0.407692 0.841463
144 SRA 0.40708 0.85
145 CMX 0.406667 0.788889
146 SCO 0.406667 0.788889
147 TYM 0.405797 0.886076
148 COD 0.405594 0.777778
149 CA6 0.405229 0.70297
150 OXK 0.405229 0.771739
151 AP2 0.405172 0.886076
152 A12 0.405172 0.886076
153 9SN 0.40458 0.853659
154 LAQ 0.404412 0.802326
155 T5A 0.404255 0.914634
156 FAM 0.403974 0.771739
157 ACO 0.403974 0.763441
158 FCX 0.403974 0.763441
159 VO4 ADP 0.403226 0.860759
160 ADP VO4 0.403226 0.860759
161 YLC 0.402878 0.823529
162 1VU 0.402597 0.763441
163 B5Y 0.401515 0.875
164 FA5 0.401515 0.886076
165 HAX 0.401316 0.771739
166 AR6 AR6 0.4 0.871795
167 CAJ 0.4 0.771739
168 AFH 0.4 0.843373
169 APU 0.4 0.923077
170 A U 0.4 0.898734
171 TXA 0.4 0.886076
172 4UU 0.4 0.948052
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5Z2L; Ligand: NDP; Similar sites found with APoc: 41
This union binding pocket(no: 1) in the query (biounit: 5z2l.bio4) has 33 residues
No: Leader PDB Ligand Sequence Similarity
1 2JAH NDP 32.7935
2 2GDZ NAD 34.2857
3 1XG5 NAP 35.102
4 3TN7 NJP 37.551
5 2BD0 NAP 37.7049
6 2JAP NDP 40.4858
7 4O0L NDP 41.0909
8 1PR9 NAP 41.8033
9 3D3W NAP 41.8033
10 3OID NDP 42.0408
11 5O42 BGC 42.8571
12 5O42 NAD 42.8571
13 5O42 9JW 42.8571
14 3SJU NDP 43.2653
15 4ITU 1HS 43.8662
16 4ITU NAI 43.8662
17 5THQ NDP 44.1176
18 1E3W NAD 44.4898
19 1E6W NAD 44.4898
20 1U7T TDT 44.898
21 1U7T NAD 44.898
22 4CQM NAP 45.7143
23 1X1T NAD 46.1224
24 4RF2 NAP 46.5306
25 1IY8 NAD 46.5306
26 4ZA2 NAD 46.5306
27 1ZK4 NAP 46.5306
28 2WSB NAD 46.9388
29 2DKN NAI 47.3469
30 6CI9 NAP 47.3469
31 1AE1 NAP 47.7551
32 5GWT NAD 48.1633
33 5GWT SIN 48.1633
34 3QWI NAP 48.5714
35 3QWI CUE 48.5714
36 2B4Q NAP 48.5714
37 1EDO NAP 48.7705
38 2ZAT NAP 48.9796
39 1NFQ NAI 49.3878
40 4QED NAP 49.3878
41 4OSP NAP 49.7959
Pocket No.: 2; Query (leader) PDB : 5Z2L; Ligand: NDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5z2l.bio4) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5Z2L; Ligand: NDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5z2l.bio6) has 34 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5Z2L; Ligand: NDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5z2l.bio6) has 34 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5Z2L; Ligand: NDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5z2l.bio2) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5Z2L; Ligand: NDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5z2l.bio2) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5Z2L; Ligand: NDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5z2l.bio5) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5Z2L; Ligand: NDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5z2l.bio5) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 5Z2L; Ligand: NDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 5z2l.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 5Z2L; Ligand: NDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 5z2l.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 5Z2L; Ligand: NDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 5z2l.bio3) has 34 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 5Z2L; Ligand: NDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 5z2l.bio3) has 33 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback