FAIRMol

MK131

Pose ID 2952 Compound 867 Pose 242

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T05
L. major PTR1 L. major
Ligand MK131
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
71.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.65, Jaccard 0.48, H-bond role recall 0.50
Burial
84%
Hydrophobic fit
66%
Reason: strain 71.8 kcal/mol
strain ΔE 71.8 kcal/mol 2 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.118 kcal/mol/HA) ✓ Good fit quality (FQ -10.55) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Extreme strain energy (71.8 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (8) ✗ Many internal clashes (10)
Score
-31.294
kcal/mol
LE
-1.118
kcal/mol/HA
Fit Quality
-10.55
FQ (Leeson)
HAC
28
heavy atoms
MW
395
Da
LogP
0.29
cLogP
Strain ΔE
71.8 kcal/mol
SASA buried
84%
Lipo contact
66% BSA apolar/total
SASA unbound
656 Ų
Apolar buried
366 Ų

Interaction summary

HB 13 HY 17 PI 1 CLASH 2

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank1.555Score-31.294
Inter norm-1.094Intra norm-0.024
Top1000noExcludedno
Contacts17H-bonds13
Artifact reasongeometry warning; 10 clashes; 8 protein contact clashes; 1 severe cofactor-context clash; high strain Δ 71.8
Residues
ARG17 ASP181 GLN186 GLY225 LEU188 LEU226 LEU229 MET183 NDP302 PHE113 PRO187 THR184 THR195 TYR191 TYR194 VAL230 ARG287

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap11Native recall0.65
Jaccard0.48RMSD-
HB strict3Strict recall0.43
HB same residue+role3HB role recall0.50
HB same residue3HB residue recall0.60

Protein summary

274 residues
Protein targetT05Atoms4108
Residues274Chains2
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:NDP302

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
255 1.4662149465789707 -0.854976 -22.2617 5 13 11 0.65 0.17 - no Open
242 1.5548221977658128 -1.09378 -31.2942 13 17 11 0.65 0.50 - no Current
308 1.9684843436506891 -0.945656 -26.3175 9 16 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -31.294kcal/mol
Ligand efficiency (LE) -1.1177kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.551
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 395.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.29
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 71.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 116.89kcal/mol
Minimised FF energy 45.10kcal/mol

SASA & burial

✓ computed
SASA (unbound) 656.1Ų
Total solvent-accessible surface area of free ligand
BSA total 552.6Ų
Buried surface area upon binding
BSA apolar 366.3Ų
Hydrophobic contacts buried
BSA polar 186.2Ų
Polar contacts buried
Fraction buried 84.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1630.7Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1018.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)