Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
27.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.95, Jaccard 0.80, H-bond role recall 0.45
Reason: no major geometry red flags detected
1 protein-contact clashes
55% of hydrophobic surface appears solvent-exposed (12/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.771 kcal/mol/HA)
✓ Good fit quality (FQ -7.28)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ High strain energy (27.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-21.594
kcal/mol
LE
-0.771
kcal/mol/HA
Fit Quality
-7.28
FQ (Leeson)
HAC
28
heavy atoms
MW
379
Da
LogP
3.88
cLogP
Final rank
2.0237
rank score
Inter norm
-1.075
normalised
Contacts
24
H-bonds 11
Interaction summary
HBA 7
HY 5
PI 1
CLASH 1
Interaction summary
HBA 7
HY 5
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 20 | Native recall | 0.95 |
| Jaccard | 0.80 | RMSD | - |
| HB strict | 7 | Strict recall | 0.47 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU: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
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.594kcal/mol
Ligand efficiency (LE)
-0.7712kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.281
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
379.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.88
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
88.26kcal/mol
Minimised FF energy
61.23kcal/mol
SASA & burial
✓ computed
SASA (unbound)
674.6Ų
Total solvent-accessible surface area of free ligand
BSA total
607.5Ų
Buried surface area upon binding
BSA apolar
516.2Ų
Hydrophobic contacts buried
BSA polar
91.3Ų
Polar contacts buried
Fraction buried
90.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1445.0Ų
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
501.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)