FAIRMol

MK219

Pose ID 14478 Compound 464 Pose 240

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
T22
L. donovani rab5a L. donovani
Ligand MK219

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
23.9 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.86, Jaccard 0.69, H-bond role recall 0.27
Burial
86%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 56% of hydrophobic surface appears solvent-exposed (14/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.682 kcal/mol/HA) ✓ Good fit quality (FQ -6.71) ✓ Good H-bonds (5 bonds) ✓ Deep burial (86% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ High strain energy (23.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-21.827
kcal/mol
LE
-0.682
kcal/mol/HA
Fit Quality
-6.71
FQ (Leeson)
HAC
32
heavy atoms
MW
438
Da
LogP
4.28
cLogP
Final rank
4.2682
rank score
Inter norm
-0.970
normalised
Contacts
23
H-bonds 13
Strain ΔE
23.9 kcal/mol
SASA buried
86%
Lipo contact
79% BSA apolar/total
SASA unbound
735 Ų
Apolar buried
501 Ų

Interaction summary

HBD 2 HBA 3 HY 3 PI 1 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

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

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
NameRAB5AContacts21
PoseOpen native poseHB0
IFP residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28
Current overlap18Native recall0.86
Jaccard0.69RMSD-
HB strict4Strict recall0.27
HB same residue+role3HB role recall0.27
HB same residue4HB residue recall0.36

Protein summary

165 residues
Protein targetT22Atoms2561
Residues165Chains1
Residue summaryLEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
364 1.829900181254628 -0.719662 -18.3424 7 15 0 0.00 0.00 - no Open
265 2.026313243924789 -1.01026 -23.2914 7 17 0 0.00 0.00 - no Open
329 2.0373471110131636 -0.869732 -22.9516 3 18 0 0.00 0.00 - no Open
330 2.058710961639984 -0.909592 -23.8784 2 20 0 0.00 0.00 - no Open
273 2.6597483939163937 -1.27139 -31.6043 10 19 0 0.00 0.00 - no Open
339 2.6953150877472445 -0.847963 -22.7415 4 18 0 0.00 0.00 - no Open
216 3.6249745621726803 -1.05167 -23.8418 13 18 0 0.00 0.00 - no Open
267 3.990038112087562 -0.793892 -22.5817 3 14 0 0.00 0.00 - no Open
240 4.268181873602591 -0.970374 -21.8269 13 23 18 0.86 0.27 - no Current
313 4.372928356142067 -0.902686 -22.7305 9 19 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 -21.827kcal/mol
Ligand efficiency (LE) -0.6821kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.708
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 437.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.28
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 59.01kcal/mol
Minimised FF energy 35.11kcal/mol

SASA & burial

✓ computed
SASA (unbound) 734.8Ų
Total solvent-accessible surface area of free ligand
BSA total 631.6Ų
Buried surface area upon binding
BSA apolar 501.5Ų
Hydrophobic contacts buried
BSA polar 130.1Ų
Polar contacts buried
Fraction buried 85.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1474.2Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 498.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)