Homology Model of Human FIXa

All structural analysis of the mutations presented within this database uses the homology model of FIXa (FIXa_HUMAN.pdb) that was generated by us from the experimental structures available for the 4 domains individually.

The PDB codes of the experimental structures for these 4 human domains are: Gla domain (PDB code: 1CFI), the EGF1 domain (PDB code: 1EDM) and the EGF2-SP domain pair (PDB code: 3KCG).

• The model was built using MODELLER 9.10 and Discovery Studio 2.5.

Experimental Structures available for HUMAN Coagulation Factor IX

PDB	Method	Description	Resolution	Chain	Position	PDBsum
1CFH	NMR	structure of the metal-free gamma-carboxyglutamic acid-rich membrane binding region of factor ix by two-dimensional nmr spectroscopy	-	A	47-93	>>
1CFI	NMR	nmr structure of calcium ion-bound gamma-carboxy-glutamic acid-rich domain of factor ix	-	A	47-93	>>
1EDM	X-ray	epidermal growth factor-like domain from human factor ix	1.50	B/C	92-130	>>
1IXA	NMR	the three-dimensional structure of the first egf-like module of human factor ix: comparison with egf and tgf-a	-	A	92-130	>>
1MGX	NMR	coagulation factor, mg(ii), nmr, 7 structures (backbone atoms only)	-	A	47-93	>>
1NL0	X-ray	crystal structure of human factor ix gla domain in complex of an inhibitory antibody, 10c12	2.20	G	47-91	>>
1RFN	X-ray	human coagulation factor ixa in complex with p-amino benzamidine	2.80	A	227-461	>>
1RFN	X-ray	human coagulation factor ixa in complex with p-amino benzamidine	2.80	B	133-188	>>
2WPH	X-ray	factor ixa superactive triple mutant	1.50	E	133-191	>>
2WPH	X-ray	factor ixa superactive triple mutant	1.50	S	227-461	>>
2WPI	X-ray	factor ixa superactive double mutant	1.99	E	133-191	>>
2WPI	X-ray	factor ixa superactive double mutant	1.99	S	227-461	>>
2WPJ	X-ray	factor ixa superactive triple mutant, nacl-soaked	1.60	E	133-191	>>
2WPJ	X-ray	factor ixa superactive triple mutant, nacl-soaked	1.60	S	227-461	>>
2WPK	X-ray	factor ixa superactive triple mutant, ethylene glycol-soaked	2.21	E	133-191	>>
2WPK	X-ray	factor ixa superactive triple mutant, ethylene glycol-soaked	2.21	S	227-461	>>
2WPL	X-ray	factor ixa superactive triple mutant, edta-soaked	1.82	E	133-191	>>
2WPL	X-ray	factor ixa superactive triple mutant, edta-soaked	1.82	S	227-461	>>
2WPM	X-ray	factor ixa superactive mutant, egr-cmk inhibited	2.00	E	133-191	>>
2WPM	X-ray	factor ixa superactive mutant, egr-cmk inhibited	2.00	S	227-461	>>
3KCG	X-ray	crystal structure of the antithrombin-factor ixa-pentasaccharide complex	1.70	H	227-461	>>
3KCG	X-ray	crystal structure of the antithrombin-factor ixa-pentasaccharide complex	1.70	L	131-188	>>
3LC3	X-ray	benzothiophene inhibitors of factor ixa	1.90	A/C	227-461	>>
3LC3	X-ray	benzothiophene inhibitors of factor ixa	1.90	B/D	133-188	>>
3LC5	X-ray	selective benzothiophine inhibitors of factor ixa	2.62	A	227-461	>>
3LC5	X-ray	selective benzothiophine inhibitors of factor ixa	2.62	B	133-188	>>
4WM0	X-ray	crystal structure of mouse xyloside xylosyltransferase 1 complexed with acceptor ligand	2.37	D	92-130	>>
4WMA	X-ray	crystal structure of mouse xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and udp-glucose	1.62	D	92-130	>>
4WMB	X-ray	crystal structure of mouse xyloside xylosyltransferase 1 complexed with manganese, acceptor ligand and udp	2.05	D	92-130	>>
4WMI	X-ray	crystal structure of mouse xyloside xylosyltransferase 1 complexed with manganese, product ligand and udp (product complex i)	1.87	D	92-130	>>
4WMK	X-ray	crystal structure of mouse xyloside xylosyltransferase 1 complexed with manganese, product ligand and udp (product complex ii)	2.08	D	92-130	>>
4WN2	X-ray	crystal structure of mouse xyloside xylosyltransferase 1 complexed with manganese, product ligand and udp (product complex iii)	1.95	D	92-130	>>
4WNH	X-ray	crystal structure of mouse xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and udp-xylose	1.95	D	92-130	>>
4YZU	X-ray	rapid development of two factor ixa inhibitors from hit to lead	1.41	A	227-461	>>
4YZU	X-ray	rapid development of two factor ixa inhibitors from hit to lead	1.41	B	130-191	>>
4Z0K	X-ray	rapid development of two factor ixa inhibitors from hit to lead	1.41	A	227-461	>>
4Z0K	X-ray	rapid development of two factor ixa inhibitors from hit to lead	1.41	B	130-191	>>
4ZAE	X-ray	development of a novel class of potent and selective fixa inhibitors	1.86	A	227-461	>>
4ZAE	X-ray	development of a novel class of potent and selective fixa inhibitors	1.86	B	130-191	>>
5EGM	X-ray	development of a novel tricyclic class of potent and selective fixa inhibitors	1.84	A	227-461	>>
5EGM	X-ray	development of a novel tricyclic class of potent and selective fixa inhibitors	1.84	B	130-191	>>
5F84	X-ray	crystal structure of drosophila poglut1 (rumi) complexed with its glycoprotein product (glucosylated egf repeat) and udp	2.50	A	21-407	>>
5F84	X-ray	crystal structure of drosophila poglut1 (rumi) complexed with its glycoprotein product (glucosylated egf repeat) and udp	2.50	B	130-191	>>
5F85	X-ray	crystal structure of drosophila poglut1 (rumi) complexed with its substrate protein (egf repeat) and udp	2.15	A	21-407	>>
5F85	X-ray	crystal structure of drosophila poglut1 (rumi) complexed with its substrate protein (egf repeat) and udp	2.15	B	92-130	>>
5F86	X-ray	crystal structure of drosophila poglut1 (rumi) complexed with its substrate protein (egf repeat)	1.90	A	21-407	>>
5F86	X-ray	crystal structure of drosophila poglut1 (rumi) complexed with its substrate protein (egf repeat)	1.90	B	92-130	>>
5JB8	X-ray	crystal structure of factor ixa variant k98t in complex with egr-chloromethylketone	1.45	E	134-191	>>
5JB8	X-ray	crystal structure of factor ixa variant k98t in complex with egr-chloromethylketone	1.45	S	227-461	>>
5JB9	X-ray	crystal structure of factor ixa k98t variant in complex with ppack	1.30	E	134-191	>>
5JB9	X-ray	crystal structure of factor ixa k98t variant in complex with ppack	1.30	S	227-461	>>
5JBA	X-ray	crystal structure of factor ixa variant v16i k98t y177t i212v in complex with ppack	1.40	E	134-191	>>
5JBA	X-ray	crystal structure of factor ixa variant v16i k98t y177t i212v in complex with ppack	1.40	S	227-461	>>
5JBB	X-ray	crystal structure of factor ixa variant v16i k98t y177t i213v in complex with egr-chloromethylketone	1.56	E	134-191	>>
5JBB	X-ray	crystal structure of factor ixa variant v16i k98t y177t i213v in complex with egr-chloromethylketone	1.56	S	227-461	>>
5JBC	X-ray	crystal structure of factor ixa variant v16i k98t y177t i213v in complex with ppack	1.90	E	134-191	>>
5JBC	X-ray	crystal structure of factor ixa variant v16i k98t y177t i213v in complex with ppack	1.90	S	227-461	>>
5TNO	X-ray	discovery of novel aminobenzisoxazole derivatives as orally available factor ixa inhibitors	1.54	A	227-461	>>
5TNO	X-ray	discovery of novel aminobenzisoxazole derivatives as orally available factor ixa inhibitors	1.54	B	130-191	>>
5TNT	X-ray	discovery of novel aminobenzisoxazole derivatives as orally available factor ixa inhibitors	1.40	A	227-461	>>
5TNT	X-ray	discovery of novel aminobenzisoxazole derivatives as orally available factor ixa inhibitors	1.40	B	130-191	>>
5VYG	X-ray	crystal structure of hfa9 egf repeat with o-glucose trisaccharide	2.20	A/B/C	92-130	>>
6MV4	X-ray	crystal structure of human coagulation factor ixa	1.37	H	227-461	>>
6MV4	X-ray	crystal structure of human coagulation factor ixa	1.37	L	132-185	>>
6RFK	X-ray	crystal structure of egrck-inhibited gla-domainless fixa (k148q, r150q variant)	1.60	E	130-191	>>
6RFK	X-ray	crystal structure of egrck-inhibited gla-domainless fixa (k148q, r150q variant)	1.60	S	227-461	>>
6X5J	X-ray	discovery of hydroxy pyrimidine factor ixa inhibitors	2.51	B	130-191	>>
6X5J	X-ray	discovery of hydroxy pyrimidine factor ixa inhibitors	2.51	A	227-461	>>
6X5L	X-ray	discovery of hydroxy pyrimidine factor ixa inhibitors	2.25	A	227-460	>>
6X5L	X-ray	discovery of hydroxy pyrimidine factor ixa inhibitors	2.25	B	130-191	>>
6X5P	X-ray	discovery of hydroxy pyrimidine factor ixa inhibitors	2.00	A	227-461	>>
6X5P	X-ray	discovery of hydroxy pyrimidine factor ixa inhibitors	2.00	B	130-191	>>
NA	prediction	alphafold structure prediction for coagulation factor ix.	NA	A	1-461	>>

Experimental Structures available for porcine Coagulation Factor IX

PDB	Method	Description	Resolution	Chain	Position	PDBsum
1PFX	X-ray	x-ray structure of clotting factor ixa: active site and module structure related to xase activity and hemophilia b.	3.00	L	1-146	>>
1PFX	X-ray	x-ray structure of clotting factor ixa: active site and module structure related to xase activity and hemophilia b.	3.00	C	183-410	>>
1X7A	X-ray	sar and factor ixa crystal structure of a dual inhibitor of factors ixa and xa.	2.90	L	1-146	>>
1X7A	X-ray	sar and factor ixa crystal structure of a dual inhibitor of factors ixa and xa.	2.90	C	183-410	>>

Experimental Structures available for bovine Coagulation Factor IX

PDB	Method	Description	Resolution	Chain	Position	PDBsum
1J34	X-ray	crystal structure of mg2+- and ca2+-bound gla domain of factor ix complexed with binding protein.	1.55	C	1-46	>>
1J35	X-ray	crystal structure of mg2+- and ca2+-bound gla domain of factor ix complexed with binding protein.	1.80	C	1-46	>>