FAIRMol

Z241739672

Pose ID 14760 Compound 4950 Pose 522

DB SELECTIONDocking 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 Z241739672

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
13.4 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.86, Jaccard 0.67, H-bond role recall 0.27
Burial
92%
Hydrophobic fit
85%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes 39% of hydrophobic surface appears solvent-exposed (7/18 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 (-1.305 kcal/mol/HA) ✓ Good fit quality (FQ -11.87) ✓ Good H-bonds (4 bonds) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Moderate strain (13.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-32.629
kcal/mol
LE
-1.305
kcal/mol/HA
Fit Quality
-11.87
FQ (Leeson)
HAC
25
heavy atoms
MW
379
Da
LogP
3.05
cLogP
Strain ΔE
13.4 kcal/mol
SASA buried
92%
Lipo contact
85% BSA apolar/total
SASA unbound
623 Ų
Apolar buried
490 Ų

Interaction summary

HB 4 HY 6 PI 1 CLASH 5 ⚠ Exposure 38%

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes
⚠️Partial hydrophobic solvent exposure
39% of hydrophobic surface appears solvent-exposed (7/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 18 Buried (contacted) 11 Exposed 7 LogP 3.05 H-bonds 4
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank3.186Score-32.629
Inter norm-1.297Intra norm-0.008
Top1000noExcludedno
Contacts24H-bonds4
Artifact reasongeometry warning; 10 clashes; 2 protein clashes
Residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLU43 GLU73 GLY23 GLY25 GLY47 GLY71 ILE46 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28 THR44 THR69

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 overlap18Native recall0.86
Jaccard0.67RMSD-
HB strict4Strict recall0.27
HB same residue+role3HB role recall0.27
HB same residue3HB residue recall0.27

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
522 0.9916044632114891 -0.761204 -18.662 4 7 0 0.00 0.00 - no Open
522 3.185540939421633 -1.29749 -32.6293 4 24 18 0.86 0.27 - no Current
548 3.2003001432800326 -0.826234 -21.2647 3 14 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 -32.629kcal/mol
Ligand efficiency (LE) -1.3052kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.865
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 378.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.05
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -70.80kcal/mol
Minimised FF energy -84.23kcal/mol

SASA & burial

✓ computed
SASA (unbound) 623.2Ų
Total solvent-accessible surface area of free ligand
BSA total 576.6Ų
Buried surface area upon binding
BSA apolar 490.4Ų
Hydrophobic contacts buried
BSA polar 86.2Ų
Polar contacts buried
Fraction buried 92.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1382.6Ų
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 500.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)