FAIRMol

OHD_TB2021_76

Pose ID 14274 Compound 4107 Pose 36

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 OHD_TB2021_76

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native strong SASA done
Strain ΔE
16.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.57, Jaccard 0.46, H-bond role recall 0.18
Burial
90%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
1 protein-contact 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 ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.120 kcal/mol/HA) ✓ Good fit quality (FQ -9.88) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Moderate strain (16.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-25.761
kcal/mol
LE
-1.120
kcal/mol/HA
Fit Quality
-9.88
FQ (Leeson)
HAC
23
heavy atoms
MW
303
Da
LogP
2.51
cLogP
Strain ΔE
16.3 kcal/mol
SASA buried
90%
Lipo contact
81% BSA apolar/total
SASA unbound
572 Ų
Apolar buried
418 Ų

Interaction summary

HB 6 HY 10 PI 0 CLASH 1 ⚠ Exposure 38%
⚠️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 2.51 H-bonds 6
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank3.371Score-25.761
Inter norm-1.316Intra norm0.196
Top1000noExcludedno
Contacts17H-bonds6
Artifact reasongeometry warning; 9 clashes; 3 protein clashes
Residues
ALA24 ALA40 ALA48 ASN41 GLN42 GLU21 GLY23 GLY25 GLY47 LEU31 LEU39 LEU51 LYS26 SER22 SER27 SER28 THR44

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

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 overlap12Native recall0.57
Jaccard0.46RMSD-
HB strict3Strict recall0.20
HB same residue+role2HB role recall0.18
HB same residue2HB residue recall0.18

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

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
70 1.736716694845178 -0.948783 -22.6203 4 11 0 0.00 0.00 - no Open
65 2.976826282107063 -0.845128 -19.5223 5 9 0 0.00 0.00 - no Open
36 3.3707797679056615 -1.3162 -25.7605 6 17 12 0.57 0.18 - 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 -25.761kcal/mol
Ligand efficiency (LE) -1.1200kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.885
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 303.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.51
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.26kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 151.35kcal/mol
Minimised FF energy 135.09kcal/mol

SASA & burial

✓ computed
SASA (unbound) 571.8Ų
Total solvent-accessible surface area of free ligand
BSA total 517.2Ų
Buried surface area upon binding
BSA apolar 417.5Ų
Hydrophobic contacts buried
BSA polar 99.7Ų
Polar contacts buried
Fraction buried 90.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1346.8Ų
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 493.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)