Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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
9.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.86, Jaccard 0.82, H-bond role recall 0.36
Reason: no major geometry red flags detected
2 protein-contact clashes
65% of hydrophobic surface is solvent-exposed (13/20 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.197 kcal/mol/HA)
✓ Good fit quality (FQ -10.88)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Moderate strain (9.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-29.932
kcal/mol
LE
-1.197
kcal/mol/HA
Fit Quality
-10.88
FQ (Leeson)
HAC
25
heavy atoms
MW
326
Da
LogP
2.77
cLogP
Interaction summary
HB 7
HY 4
PI 0
CLASH 2
⚠ Exposure 65%
Interaction summary
HB 7
HY 4
PI 0
CLASH 2
⚠ Exposure 65%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (13/20 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 20
Buried (contacted) 7
Exposed 13
LogP 2.77
H-bonds 7
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)phenyl (2/5 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 2.097 | Score | -29.932 |
|---|---|---|---|
| Inter norm | -1.212 | Intra norm | 0.015 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 7 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash | ||
| Residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
ASP160
GLN42
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER27
SER28
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| 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 | 18 | Native recall | 0.86 |
| Jaccard | 0.82 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 676 | -0.2008936714302171 | -1.43465 | -34.8564 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 660 | 0.46007232838639606 | -1.02491 | -26.2027 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 678 | 0.8796915712031312 | -1.01561 | -23.9951 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 665 | 1.228388032666358 | -1.2817 | -29.3257 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 660 | 1.7403331477794532 | -0.965961 | -23.8553 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 661 | 2.0730042543206704 | -1.0933 | -26.1437 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 678 | 2.096965528731848 | -1.2124 | -29.932 | 7 | 19 | 18 | 0.86 | 0.36 | - | no | Current |
| 672 | 2.4180673824662544 | -1.14541 | -28.0703 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 671 | 2.4771333975395495 | -0.992363 | -24.8643 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 679 | 2.5572498642857204 | -1.22014 | -29.4993 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 667 | 2.6594168436889833 | -1.12471 | -25.0382 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.932kcal/mol
Ligand efficiency (LE)
-1.1973kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.884
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
326.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.77
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
61.33kcal/mol
Minimised FF energy
52.23kcal/mol
SASA & burial
✓ computed
SASA (unbound)
584.4Ų
Total solvent-accessible surface area of free ligand
BSA total
486.7Ų
Buried surface area upon binding
BSA apolar
361.9Ų
Hydrophobic contacts buried
BSA polar
124.9Ų
Polar contacts buried
Fraction buried
83.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1307.8Ų
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
513.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)