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Receptor
PDB id Resolution Class Description Source Keywords
3QXV 2.5 Å NON-ENZYME: OTHER STRUCTURE OF AN ANTI-METHOTREXATE CDR1-4 GRAFT VHH ANTIBODY WITH METHOTREXATE LAMA GLAMA CAMELID SINGLE DOMAIN ANTIBODY HEAVY CHAIN ONLY VHH ANTIBANTI-HAPTEN ANTIBODY CDRHAPTEN BINDING SMALL MOLECULE SELIGAND BINDING LOW MOLECULAR WEIGHT COMPOUND METHOTREXATESYSTEM
Ref.: AN ANTI-HAPTEN CAMELID ANTIBODY REVEALS A CRYPTIC B SITE WITH SIGNIFICANT ENERGETIC CONTRIBUTIONS FROM NONHYPERVARIABLE LOOP. PROTEIN SCI. V. 20 1196 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MTX A:2000;
B:2000;
C:2000;
D:2000;
E:2000;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
Kd = 5 nM
454.439 C20 H22 N8 O5 CN(Cc...
SO4 A:3000;
B:3000;
B:3001;
C:3000;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
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
3QXV 2.5 Å NON-ENZYME: OTHER STRUCTURE OF AN ANTI-METHOTREXATE CDR1-4 GRAFT VHH ANTIBODY WITH METHOTREXATE LAMA GLAMA CAMELID SINGLE DOMAIN ANTIBODY HEAVY CHAIN ONLY VHH ANTIBANTI-HAPTEN ANTIBODY CDRHAPTEN BINDING SMALL MOLECULE SELIGAND BINDING LOW MOLECULAR WEIGHT COMPOUND METHOTREXATESYSTEM
Ref.: AN ANTI-HAPTEN CAMELID ANTIBODY REVEALS A CRYPTIC B SITE WITH SIGNIFICANT ENERGETIC CONTRIBUTIONS FROM NONHYPERVARIABLE LOOP. PROTEIN SCI. V. 20 1196 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 3QXT Kd = 6700 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
2 3QXV Kd = 5 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 62 families.
1 1QD0 - RR6 C35 H25 N9 O22 S6 c1cc(c(cc1....
2 1I3U - RR1 C19 H16 N8 O10 S3 c1ccc(c(c1....
3 5VM0 ic50 = 19 nM 9EG C13 H9 Cl3 N2 O c1cc(ccc1N....
4 3QXT Kd = 6700 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
5 3QXV Kd = 5 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
6 2X6M - GLY TYR GLN ASP TYR GLU PRO GLU ALA n/a n/a
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 1QD0 - RR6 C35 H25 N9 O22 S6 c1cc(c(cc1....
2 1I3U - RR1 C19 H16 N8 O10 S3 c1ccc(c(c1....
3 5VM6 ic50 = 78 nM 9EG C13 H9 Cl3 N2 O c1cc(ccc1N....
4 5VM0 ic50 = 19 nM 9EG C13 H9 Cl3 N2 O c1cc(ccc1N....
5 3LN9 - FLC C6 H5 O7 C(C(=O)[O-....
6 3QXT Kd = 6700 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
7 3QXV Kd = 5 nM MTX C20 H22 N8 O5 CN(Cc1cnc2....
8 2X6M - GLY TYR GLN ASP TYR GLU PRO GLU ALA n/a n/a
9 5VL2 ic50 = 20 nM 9EG C13 H9 Cl3 N2 O c1cc(ccc1N....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MTX; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 MTX 1 1
2 3BI 0.783505 0.884058
3 2MX 0.778947 0.924242
4 04J 0.663043 0.870968
5 MT1 0.632653 0.968254
6 MOT 0.534653 0.923077
7 COP 0.453782 0.815385
8 FOL 0.410714 0.779412
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3QXV; Ligand: MTX; Similar sites found with APoc: 171
This union binding pocket(no: 1) in the query (biounit: 3qxv.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 6B79 ORA None
2 6FA4 D1W None
3 5CLO NS8 None
4 1MFI FHC None
5 5O1I 9GH None
6 1V3S ATP None
7 3I3X U22 None
8 2Y7P SAL None
9 4RQL SNE None
10 3ZF8 GDP None
11 1C3X 8IG None
12 3EM0 CHD None
13 5DX0 SFG None
14 1QKQ MAN None
15 3ZO7 K6H None
16 3GXW SIN None
17 5OCG 9R5 None
18 2YN4 39J None
19 6F4W FMC None
20 3G89 SAM None
21 5W10 CMP None
22 5FUI APY 1.5873
23 1ZNY GDP 1.5873
24 3ESS 18N 1.5873
25 3QSB 743 1.5873
26 3E2M E2M 1.5873
27 4ZTD ALA GLY ALA GLY ALA 2.38095
28 1VMK GUN 2.38095
29 5HWV MBN 2.38095
30 3VKX T3 2.38095
31 4L3L 5FI 2.38095
32 3A4T SFG 2.38095
33 4GJ3 0XP 2.38095
34 3IWD M2T 2.94118
35 1SBR VIB 3.1746
36 4B2Z P5S 3.1746
37 2BJU IH4 3.1746
38 3PP0 03Q 3.1746
39 4M52 FAD 3.1746
40 4XPQ FUL 3.1746
41 4NOS ITU 3.1746
42 1UPR 4IP 3.25203
43 6GNO XDI 3.96825
44 1SDW IYT 3.96825
45 1MJT ITU 3.96825
46 4KBA 1QM 3.96825
47 5W4W 9WG 3.96825
48 5BVE 4VG 3.96825
49 1USF NAP 3.96825
50 3D91 REM 3.96825
51 5IFK HPA 3.96825
52 1O9P MLA 3.96825
53 1RZM E4P 3.96825
54 2WOX NDP 3.96825
55 4CQE CQE 3.96825
56 3CM2 X23 3.96825
57 3CBC DBS 4.7619
58 4WHZ 3NL 4.7619
59 1XXR MAN 4.7619
60 3TW1 AHN 4.7619
61 4XTX 590 4.7619
62 5TH5 MET 4.7619
63 1GG6 APL 4.7619
64 4YRI 4JH 4.7619
65 2WEL K88 4.7619
66 3A16 PXO 4.7619
67 2Y6Q I7T 4.7619
68 1GJC 130 4.7619
69 2Z9I GLY ALA THR VAL 4.7619
70 2CJA ATP 4.7619
71 3TTI KBI 4.7619
72 5TUF TDC 4.7619
73 1GPM AMP 4.7619
74 5Y4R C2E 4.7619
75 3E7O 35F 4.7619
76 1NME 159 4.7619
77 5TZO 7V7 4.7619
78 4D7E FAD 4.7619
79 1R6T TYM 4.7619
80 1LSH PLD 5.55556
81 5KJW 53C 5.55556
82 5G48 1FL 5.55556
83 2XG5 EC5 5.55556
84 2XG5 EC2 5.55556
85 2IOY RIP 5.55556
86 1QO8 FAD 5.55556
87 3RNM FAD 5.55556
88 2F5Z FAD 5.55556
89 4ZVV NAD 5.55556
90 4ZVV GN0 5.55556
91 3UOY FAD 5.55556
92 3UOY NAP 5.55556
93 1UYY BGC BGC 5.55556
94 2C6Q NDP 5.55556
95 4FFG 0U8 6.34921
96 6ACS CIT 6.34921
97 1G51 AMP 6.34921
98 4IXW IXW 6.34921
99 3AI3 SOE 6.34921
100 3NZ1 3NY 6.34921
101 1RSG FAD 6.34921
102 2XVD AS6 6.34921
103 4TWP AXI 6.34921
104 1YY5 FAD 6.34921
105 5H2U 1N1 6.34921
106 2MSB NAG BMA MAN MAN MAN MAN MAN 6.95652
107 4ZJS 4P0 7.14286
108 1NB9 ADP 7.14286
109 1NB9 RBF 7.14286
110 2YNE YNE 7.14286
111 2YNE NHW 7.14286
112 3G5D 1N1 7.14286
113 3DLG GWE 7.14286
114 1VJY 460 7.14286
115 1HXD BTN 7.14286
116 5LXB 7A9 7.14286
117 4WOE ADP 7.14286
118 1DRJ RIP 7.14286
119 1OFL NGK GCD 7.93651
120 1WPY BTN 7.93651
121 6GWR FEW 7.93651
122 2DXU BT5 7.93651
123 4X3R 686 7.93651
124 1SES AMP 7.93651
125 3VRY B43 7.93651
126 1TT8 PHB 7.93651
127 2BKX F6R 7.93651
128 1WOR RED 8.73016
129 3ZJX BOG 8.73016
130 5MW4 5JU 8.73016
131 2RCU BUJ 8.73016
132 1JQ3 AAT 8.73016
133 6GAS FAD 8.73016
134 1OUK 084 9.52381
135 2Z3U CRR 9.52381
136 1K7V NAG GAL BGC 9.52381
137 5F2T PLM 9.52381
138 4MOB ADP 10.3175
139 2VL1 GLY GLY 10.3175
140 3KU0 ADE 10.3175
141 5HCY 60D 10.3175
142 1Y8Q ATP 11.1111
143 6EK3 OUL 11.1111
144 4EWN 0VR 11.1111
145 5F7J ADE 11.9048
146 4NJH SAM 11.9048
147 4NJH 2K8 11.9048
148 4N70 2HX 12.6984
149 1EP2 ORO 12.6984
150 2XCG XCG 12.6984
151 6I6X TLA 12.6984
152 2EB5 OXL 12.6984
153 4P5Z Q7M 12.6984
154 1RJW ETF 13.4921
155 4A0M NAD 13.4921
156 3I7V B4P 14.2857
157 5L2R MLA 14.2857
158 3TCT 3MI 14.2857
159 3OV6 MK0 14.2857
160 3SAO DBH 15.0794
161 3ITA AIC 15.0794
162 6C0B PAM 15.0794
163 2QPU QPU 15.0794
164 2QPU QPS 15.0794
165 4C2W ANP 15.3846
166 1XX4 BAM 15.873
167 3MYZ TFX 18
168 4HE2 AMP 18.254
169 6EWZ APC 19.0476
170 3RWP ABQ 19.0476
171 3T0W DIW 41.4634
Pocket No.: 2; Query (leader) PDB : 3QXV; Ligand: MTX; Similar sites found with APoc: 155
This union binding pocket(no: 2) in the query (biounit: 3qxv.bio3) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 6ARJ BW4 None
2 6ARJ SAH None
3 1MJH ATP None
4 6GAR FAD None
5 1KGI T4A None
6 4FE2 AIR None
7 1YZQ GNP None
8 1LNX URI None
9 4CNK FAD None
10 1IDA 0PO None
11 2Z3Y F2N 1.5873
12 5M67 ADE 1.5873
13 5M67 3D1 1.5873
14 5M67 NAD 1.5873
15 2WLG SOP 2.38095
16 5XDT ZI7 2.38095
17 4I3V NAD 2.38095
18 3SFI 3SF 2.38095
19 4QAC KK3 2.38095
20 1P1C SAH 3.1746
21 3AB1 FAD 3.1746
22 4XZ6 TMO 3.1746
23 2NXE SAM 3.1746
24 1KZN CBN 3.1746
25 3RAB GNP 3.1746
26 1OMO NAD 3.1746
27 3O9L LPN 3.96825
28 4H2W 5GP 3.96825
29 3VBK COA 3.96825
30 4B0T ADP 3.96825
31 3HDY FAD 3.96825
32 3HDY GDU 3.96825
33 4UCI ADN 3.96825
34 3HDY FDA 3.96825
35 6GFK SAH 3.96825
36 5N5S NAP 3.96825
37 3C3D FO1 4.7619
38 5TUF FAD 4.7619
39 2Q7V FAD 4.7619
40 2VVL FAD 4.7619
41 3X0D SAH 4.7619
42 5XLY C2E 4.7619
43 2R4J 13P 4.7619
44 2R4J FAD 4.7619
45 2YC5 6BC 4.7619
46 2VVM FAD 4.7619
47 4Z24 FAD 4.7619
48 3H0L ADP 4.7619
49 1A5Z FBP 4.7619
50 3PA8 621 4.7619
51 4ONA UW1 4.7619
52 1O9J NAD 5.55556
53 3E5P PPI 5.55556
54 4Z87 GDP 5.55556
55 6B5G NAD 5.55556
56 6B5G CQY 5.55556
57 5J5Z FAD 5.55556
58 1F76 FMN 5.55556
59 1VDC FAD 5.55556
60 2BJK NAD 5.55556
61 5IVE 6E8 5.55556
62 1NAA 6FA 5.55556
63 2IMP NAI 5.55556
64 2I7C AAT 6.34921
65 3BZ3 YAM 6.34921
66 4TXI FAD 6.34921
67 3HXU A5A 6.34921
68 5C9P FUC 6.34921
69 1GQG DCD 6.34921
70 3VZ3 NAP 6.34921
71 4GID 0GH 6.34921
72 2NPX FAD 6.34921
73 2NPX NAD 6.34921
74 3VZ3 SSN 6.34921
75 4PLT NAI 6.34921
76 4PLT OXM 6.34921
77 1OX5 1PR 6.34921
78 4RD0 GDP 6.34921
79 5FPE 3TR 7.14286
80 1V8B NAD 7.14286
81 4IEN GDP 7.14286
82 1KDK DHT 7.14286
83 3ICS FAD 7.14286
84 2IU8 PLM 7.14286
85 3KV8 FAH 7.14286
86 3T1A 5MA 7.14286
87 3ICR FAD 7.14286
88 5L13 6ZE 7.14286
89 3MVH WFE 7.14286
90 5XVG 8FX 7.14286
91 5BW4 SAM 7.14286
92 1F5F DHT 7.14286
93 6B9R 2HE 7.93651
94 4RF7 ARG 7.93651
95 5FWA J7C 7.93651
96 5A0U CHT 7.93651
97 1XHC FAD 7.93651
98 2JLD AG1 7.93651
99 4C3Y FAD 7.93651
100 3EFS BTN 8.73016
101 2QIA U20 8.73016
102 3GC8 B45 8.73016
103 4HA6 FAD 8.73016
104 1EZ0 NAP 8.73016
105 2GU8 796 8.73016
106 5HW4 SAM 8.73016
107 4I8P NAD 9.52381
108 5XLS URA 9.52381
109 4DXD 9PC 9.52381
110 1KPG SAH 9.52381
111 2UUU PL3 9.52381
112 3AD8 NAD 9.52381
113 2RAB FAD 9.52381
114 4MVK ACE VAL PHE PHE ALA GLU ASP NH2 9.52381
115 6D6L FY4 9.52381
116 5YBL AKG 9.52381
117 1KJ1 MAN 10.0917
118 1LVL NAD 10.3175
119 3E9I XAH 10.3175
120 2GJ5 VD3 11.1111
121 3FSY SCA 11.1111
122 1BC5 ACE ASN TRP GLU THR PHE 11.1111
123 1PJ6 FOL 11.1111
124 6B9T 2HE 11.1111
125 4PAB THG 11.1111
126 5TTJ FAD 11.9048
127 5UKL SIX 11.9048
128 2GAG NAD 11.9048
129 3HAZ FAD 11.9048
130 1EP2 FMN 12.6984
131 1RM6 FAD 12.6984
132 4LH0 GLV 12.6984
133 2NVK FAD 12.6984
134 4PXL NAD 13.4921
135 4ITH RCM 13.4921
136 5M45 AMP 13.4921
137 1I8T FAD 14.2857
138 3G08 FEE 14.2857
139 5LRT ADP 14.2857
140 4BLW SAH 14.2857
141 4X60 SFG 15.0794
142 4X60 3XV 15.0794
143 3JZ4 NAP 15.0794
144 4JDR FAD 15.873
145 4ZCC FAD 16.6667
146 5IUW IAC 17.4603
147 5G5G FAD 18.254
148 4DQ2 BTX 18.254
149 1COY FAD 19.0476
150 5K8P 6R8 19.0476
151 1L0I PSR 20.5128
152 4NV7 COA 22.2222
153 2CYC TYR 25.3968
154 4GQB 0XU 31.8182
155 5FA5 MTA 35
Pocket No.: 3; Query (leader) PDB : 3QXV; Ligand: MTX; Similar sites found with APoc: 36
This union binding pocket(no: 3) in the query (biounit: 3qxv.bio5) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 1HBK MYR None
2 5TPV TYD None
3 5HZ9 5M8 None
4 3JU6 ANP 2.38095
5 3I9U DTU 2.38095
6 3IT7 TLA 2.38095
7 6G5Q EMZ 3.1746
8 3HSS MLA 3.1746
9 3JQ9 AX1 3.96825
10 3BMO AX4 3.96825
11 4RPL 3UC 3.96825
12 4RPL FAD 3.96825
13 3E7S AT2 3.96825
14 4BTV RB3 3.96825
15 2CE7 ADP 4.7619
16 2JDR L20 4.7619
17 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 4.7619
18 3ZS9 ADP ALF 4.7619
19 3MJY IJZ 4.7619
20 3MJY FMN 4.7619
21 3G1Z AMP 5.55556
22 2ZMF CMP 5.55556
23 3P2H NOO 5.55556
24 2F6D ACR 6.34921
25 1XS1 DUT 6.34921
26 3W54 RNB 6.34921
27 3QPB URA 7.93651
28 3A23 GAL 7.93651
29 2GQS C2R 9.52381
30 5TV6 PML 9.52381
31 1IHU ADP 10.3175
32 2O07 MTA 11.1111
33 2O07 SPD 11.1111
34 5FAW CHT 11.1111
35 4L77 CNL 23.0159
36 4WO4 JLS 46.0317
Pocket No.: 4; Query (leader) PDB : 3QXV; Ligand: MTX; Similar sites found with APoc: 14
This union binding pocket(no: 4) in the query (biounit: 3qxv.bio4) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 1L5Y BEF None
2 1X0P FAD None
3 5DQ8 FLF 2.5
4 4CJN QNZ 3.1746
5 5LX6 78P 3.1746
6 2OEM 1AE 3.96825
7 2TOH HBI 4.7619
8 3F3E LEU 5.55556
9 4URS C2E 6.34921
10 1B09 PC 7.93651
11 1K7U NAG NAG 9.52381
12 4D52 GIV 10.3175
13 4D52 GXL 10.3175
14 5WL1 CUY 18.1818
Pocket No.: 5; Query (leader) PDB : 3QXV; Ligand: MTX; Similar sites found with APoc: 20
This union binding pocket(no: 5) in the query (biounit: 3qxv.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 6C5F 7L9 None
2 1MID LAP None
3 3HAD NAD None
4 3I6B KDO 1.5873
5 4JGP PYR 2.38095
6 5EW9 5VC 3.1746
7 1F9V ADP 3.1746
8 4A91 GLU 3.1746
9 2WD7 VGD 3.96825
10 5X8G S0N 4.7619
11 4FHT DHB 5.55556
12 3RHJ NAP 6.34921
13 3WV1 WHH 6.34921
14 1RO7 CSF 6.34921
15 4MIB 28M 7.14286
16 4Y3O OGA 7.14286
17 3HKW IX6 7.93651
18 5VNF VAL THR SER VAL VAL 7.93651
19 1IHU AF3 10.3175
20 2Z5Y HRM 12.6984
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