FAIRMol

Z56865835

Pose ID 14645 Compound 5190 Pose 407

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 Z56865835

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
29.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.86, Jaccard 0.82, H-bond role recall 0.45
Burial
70%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 57% of hydrophobic surface appears solvent-exposed (12/21 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 (-0.936 kcal/mol/HA) ✓ Good fit quality (FQ -9.21) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (70% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ High strain energy (29.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-29.957
kcal/mol
LE
-0.936
kcal/mol/HA
Fit Quality
-9.21
FQ (Leeson)
HAC
32
heavy atoms
MW
455
Da
LogP
1.57
cLogP
Final rank
4.6925
rank score
Inter norm
-0.952
normalised
Contacts
19
H-bonds 9
Strain ΔE
29.4 kcal/mol
SASA buried
70%
Lipo contact
74% BSA apolar/total
SASA unbound
746 Ų
Apolar buried
386 Ų

Interaction summary

HBD 1 HBA 6 HY 2 PI 1 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 6.

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
Jaccard0.82RMSD-
HB strict7Strict recall0.47
HB same residue+role5HB role recall0.45
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
407 4.692457437454324 -0.951831 -29.9571 9 19 18 0.86 0.45 - no Current
372 6.159336665420304 -1.03078 -19.7996 11 24 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 -29.957kcal/mol
Ligand efficiency (LE) -0.9362kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.206
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 454.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.57
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 28.28kcal/mol
Minimised FF energy -1.12kcal/mol

SASA & burial

✓ computed
SASA (unbound) 745.7Ų
Total solvent-accessible surface area of free ligand
BSA total 518.3Ų
Buried surface area upon binding
BSA apolar 386.2Ų
Hydrophobic contacts buried
BSA polar 132.1Ų
Polar contacts buried
Fraction buried 69.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1435.1Ų
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 522.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)