FAIRMol

MK16

Pose ID 14458 Compound 365 Pose 220

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 MK16

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
23.1 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.90, Jaccard 0.79, H-bond role recall 0.36
Burial
86%
Hydrophobic fit
83%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes 61% of hydrophobic surface is solvent-exposed (14/23 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.936 kcal/mol/HA) ✓ Good fit quality (FQ -8.93) ✓ Good H-bonds (5 bonds) ✓ Deep burial (86% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ High strain energy (23.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-27.133
kcal/mol
LE
-0.936
kcal/mol/HA
Fit Quality
-8.93
FQ (Leeson)
HAC
29
heavy atoms
MW
397
Da
LogP
3.64
cLogP
Final rank
4.9996
rank score
Inter norm
-1.090
normalised
Contacts
22
H-bonds 11
Strain ΔE
23.1 kcal/mol
SASA buried
86%
Lipo contact
83% BSA apolar/total
SASA unbound
688 Ų
Apolar buried
490 Ų

Interaction summary

HBD 3 HBA 2 HY 4 PI 1 CLASH 5

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.

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 overlap19Native recall0.90
Jaccard0.79RMSD-
HB strict4Strict recall0.27
HB same residue+role4HB role recall0.36
HB same residue5HB residue recall0.45

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
218 0.8702932048363431 -0.908629 -24.464 4 18 0 0.00 0.00 - no Open
299 2.0379983094372447 -0.947945 -23.6822 3 18 0 0.00 0.00 - no Open
317 2.1527347432726276 -0.941543 -26.1251 3 17 0 0.00 0.00 - no Open
240 2.2587325616107607 -0.832091 -21.6042 4 13 0 0.00 0.00 - no Open
240 3.2818274910563994 -0.786521 -18.603 7 16 0 0.00 0.00 - no Open
177 3.5557639252536166 -1.14994 -28.0313 10 21 0 0.00 0.00 - no Open
260 3.6013232851727364 -0.851461 -20.5074 10 18 0 0.00 0.00 - no Open
220 4.999612194010174 -1.09022 -27.133 11 22 19 0.90 0.36 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -27.133kcal/mol
Ligand efficiency (LE) -0.9356kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.931
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 397.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.64
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 41.10kcal/mol
Minimised FF energy 18.00kcal/mol

SASA & burial

✓ computed
SASA (unbound) 688.3Ų
Total solvent-accessible surface area of free ligand
BSA total 591.0Ų
Buried surface area upon binding
BSA apolar 489.5Ų
Hydrophobic contacts buried
BSA polar 101.5Ų
Polar contacts buried
Fraction buried 85.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1440.3Ų
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 502.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)