FAIRMol

Z49605089

Pose ID 14876 Compound 2446 Pose 638

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 Z49605089

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
24.2 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.71, Jaccard 0.60, H-bond role recall 0.55
Burial
84%
Hydrophobic fit
73%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.146 kcal/mol/HA) ✓ Good fit quality (FQ -10.94) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ High strain energy (24.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-33.240
kcal/mol
LE
-1.146
kcal/mol/HA
Fit Quality
-10.94
FQ (Leeson)
HAC
29
heavy atoms
MW
418
Da
LogP
1.14
cLogP
Final rank
3.3000
rank score
Inter norm
-1.209
normalised
Contacts
19
H-bonds 11
Strain ΔE
24.2 kcal/mol
SASA buried
84%
Lipo contact
73% BSA apolar/total
SASA unbound
683 Ų
Apolar buried
424 Ų

Interaction summary

HBA 6 HY 4 PI 1 CLASH 5

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: 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 overlap15Native recall0.71
Jaccard0.60RMSD-
HB strict8Strict recall0.53
HB same residue+role6HB role recall0.55
HB same residue7HB residue recall0.64

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
607 0.7883854153673052 -0.820122 -23.177 4 16 0 0.00 0.00 - no Open
618 2.785578027503189 -1.17956 -30.0286 7 21 0 0.00 0.00 - no Open
614 3.04043421104034 -0.788601 -18.3671 4 11 0 0.00 0.00 - no Open
638 3.2999969963693108 -1.20946 -33.2396 11 19 15 0.71 0.55 - no Current
628 3.6714347479305753 -0.884447 -24.2424 10 15 1 0.05 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 -33.240kcal/mol
Ligand efficiency (LE) -1.1462kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.941
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 418.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.14
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 14.52kcal/mol
Minimised FF energy -9.71kcal/mol

SASA & burial

✓ computed
SASA (unbound) 683.2Ų
Total solvent-accessible surface area of free ligand
BSA total 577.2Ų
Buried surface area upon binding
BSA apolar 423.8Ų
Hydrophobic contacts buried
BSA polar 153.3Ų
Polar contacts buried
Fraction buried 84.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1371.2Ų
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 505.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)