FAIRMol

MK172

Pose ID 2292 Compound 1785 Pose 259

DB SELECTIONDocking 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
T04
L. major PTR1 L. major
Ligand MK172
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
16.4 kcal/mol
Protein clashes
0
Internal clashes
20
Native overlap
contact recall 0.63, Jaccard 0.60, H-bond role recall 0.00
Burial
74%
Hydrophobic fit
84%
Reason: 20 internal clashes
20 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.748 kcal/mol/HA) ✓ Good fit quality (FQ -7.43) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Moderate strain (16.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (20)
Score
-24.698
kcal/mol
LE
-0.748
kcal/mol/HA
Fit Quality
-7.43
FQ (Leeson)
HAC
33
heavy atoms
MW
439
Da
LogP
5.92
cLogP
Strain ΔE
16.4 kcal/mol
SASA buried
74%
Lipo contact
84% BSA apolar/total
SASA unbound
743 Ų
Apolar buried
463 Ų

Interaction summary

HB 1 HY 24 PI 3 CLASH 0
Final rank1.250Score-24.698
Inter norm-0.849Intra norm0.100
Top1000noExcludedno
Contacts13H-bonds1
Artifact reasongeometry warning; 20 clashes
Residues
ARG17 ASP232 HIS241 LEU188 LEU226 LEU229 MET233 NDP302 PHE113 SER111 TYR194 VAL230 ARG287

Protein summary

308 residues
Protein targetT04Atoms4210
Residues308Chains3
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

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name7PXXContacts19
PoseOpen native poseHB0
IFP residues
ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER112 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap12Native recall0.63
Jaccard0.60RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue1HB residue recall0.20

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
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
259 1.2497707324385667 -0.848591 -24.6982 1 13 12 0.63 0.00 - no Current
278 2.430330756882116 -0.740586 -18.816 12 14 0 0.00 0.00 - no Open
297 3.321419821143468 -0.731548 -21.3962 5 14 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 -24.698kcal/mol
Ligand efficiency (LE) -0.7484kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.426
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 438.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.92
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 89.14kcal/mol
Minimised FF energy 72.70kcal/mol

SASA & burial

✓ computed
SASA (unbound) 742.9Ų
Total solvent-accessible surface area of free ligand
BSA total 552.8Ų
Buried surface area upon binding
BSA apolar 462.6Ų
Hydrophobic contacts buried
BSA polar 90.2Ų
Polar contacts buried
Fraction buried 74.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1803.2Ų
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 1024.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)