FAIRMol

Z44426251

Pose ID 14614 Compound 3797 Pose 376

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 Z44426251

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
32.5 kcal/mol
Protein clashes
10
Internal clashes
10
Native overlap
contact recall 0.76, Jaccard 0.53, H-bond role recall 0.09
Burial
89%
Hydrophobic fit
84%
Reason: 10 protein-contact clashes, 10 internal clashes
10 protein-contact clashes 10 intramolecular clashes 52% of hydrophobic surface appears solvent-exposed (15/29 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 (-0.794 kcal/mol/HA) ✓ Good fit quality (FQ -8.07) ✓ Good H-bonds (3 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Very high strain energy (32.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (17)
Score
-28.582
kcal/mol
LE
-0.794
kcal/mol/HA
Fit Quality
-8.07
FQ (Leeson)
HAC
36
heavy atoms
MW
501
Da
LogP
5.91
cLogP
Final rank
4.2785
rank score
Inter norm
-0.920
normalised
Contacts
25
H-bonds 7
Strain ΔE
32.5 kcal/mol
SASA buried
89%
Lipo contact
84% BSA apolar/total
SASA unbound
804 Ų
Apolar buried
602 Ų

Interaction summary

HBD 2 HBA 1 HY 6 PI 1 CLASH 10

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: strict.
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 overlap16Native recall0.76
Jaccard0.53RMSD-
HB strict1Strict recall0.07
HB same residue+role1HB role recall0.09
HB same residue2HB residue recall0.18

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
498 2.2188366637011128 -0.721545 -26.2092 2 17 0 0.00 0.00 - no Open
412 2.531371937867769 -0.579105 -18.9608 6 13 0 0.00 0.00 - no Open
372 3.5420182475646125 -0.80261 -29.1994 6 20 0 0.00 0.00 - no Open
372 3.6308207497290756 -0.748195 -16.7183 5 17 0 0.00 0.00 - no Open
376 4.278459254451291 -0.919621 -28.5817 7 25 16 0.76 0.09 - no Current
403 4.364535617432776 -0.55661 -19.9115 4 14 0 0.00 0.00 - no Open
388 4.5017657420186294 -0.69997 -21.8599 5 15 0 0.00 0.00 - no Open
367 5.176797600658553 -0.772899 -26.7623 10 16 0 0.00 0.00 - no Open
341 5.840278013669095 -0.96277 -35.9737 7 23 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 -28.582kcal/mol
Ligand efficiency (LE) -0.7939kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.069
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 501.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.91
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 86.47kcal/mol
Minimised FF energy 53.97kcal/mol

SASA & burial

✓ computed
SASA (unbound) 804.4Ų
Total solvent-accessible surface area of free ligand
BSA total 712.8Ų
Buried surface area upon binding
BSA apolar 601.9Ų
Hydrophobic contacts buried
BSA polar 110.9Ų
Polar contacts buried
Fraction buried 88.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1548.2Ų
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 505.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)